RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Source Organism Taxonomy Name (Full Lineage) = "Haemophilus influenzae Rd KW20"

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 1,811 Structures.

Refinements

Structure Determination Methodology

	computational (1,662)
	experimental (149)

CSM Source Database

AlphaFoldDB (1,662)

pLDDT Global Quality Score

	< 50.0 (1)
	50.0 - 70.0 (37)
	70.0 - 90.0 (555)
	> 90.0 (1,069)

Scientific Name of Source Organism

	Haemophilus influenzae Rd KW20 (1,810)
	synthetic construct (5)
	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (4)
	Salmonella enterica subsp. enterica serovar Typhimurium (3)
	Thermotoga maritima MSB8 (3)
	Homo sapiens (2)
	Human immunodeficiency virus 1 (2)
	Haemophilus influenzae (1)
	Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (1)
	Ligilactobacillus salivarius UCC118 (1)

More...

Taxonomy

	Bacteria (1,811)
	other sequences (5)
	Eukaryota (3)
	Riboviria (2)

Experimental Method

	X-RAY DIFFRACTION (147)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

	Protein (1,811)
	DNA (9)
	RNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (8)
	1.5 - 2.0 (59)
	2.0 - 2.5 (52)
	2.5 - 3.0 (23)
	3.0 - 3.5 (6)
	4.0 - 4.5 (1)

Release Date

	2000 - 2004 (14)
	2005 - 2009 (6)
	2010 - 2014 (19)
	2015 - 2019 (85)
	2020 - 2024 (1,687)

Enzyme Classification Name

	Transferases (337)
	Hydrolases (204)
	Oxidoreductases (100)
	Ligases (73)
	Lyases (75)
	Isomerases (64)
	Translocases (39)

Membrane Protein Annotation

	MemProtMD (3)
	PDBTM (3)
	OPM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (1,697)
	Cyclic (115)
	Dihedral (8)

SCOP Classification

	Alpha and beta proteins (a/b) (79)
	Alpha and beta proteins (a+b) (22)
	Artifacts (39)
	All beta proteins (14)

AllSelected

1 to 25 of 1,811 Structures

Page 1 of 73

Sort by

Explore in 3D

1GQZ \| pdb_00001gqz	Download File View File

Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A

Roper, D.I., Huyton, T., Turkenburg, J.P.

(2004) Acta Crystallogr D Biol Crystallogr 60: 397-400

Released	2003-06-12
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	DIAMINOPIMELATE EPIMERASE (protein)

Explore in 3D

1IM8 \| pdb_00001im8	Download File View File

Crystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine

Lim, K., Zhang, H., Tempczyk, A., Bonander, N., Toedt, J., Howard, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

(2001) Proteins 45: 397-407

Released	2001-11-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	YecO (protein)
Unique Ligands	CL, SAI

Explore in 3D

1J7G \| pdb_00001j7g	Download File View File

Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase

Lim, K., Herzberg, O., Structure 2 Function Project (S2F)

(2003) J Biological Chem 278: 13496-13502

Released	2003-04-22
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	D-tyrosyl-tRNA(Tyr) deacylase (protein)

Explore in 3D

1J85 \| pdb_00001j85	Download File View File

Structure of YibK from Haemophilus influenzae (HI0766), a truncated sequence homolog of tRNA (guanosine-2'-O-) methyltransferase (SpoU)

Lim, K., Zhang, H., Toedt, J., Tempcyzk, A., Krajewski, W., Howard, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

(2003) Proteins 51: 56-67

Released	2003-02-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	YibK (protein)

Explore in 3D

1J8B \| pdb_00001j8b	Download File View File

Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function

Lim, K., Tempcyzk, A., Toedt, J., Parsons, J.F., Howard, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

(2003) Proteins 50: 375-379

Released	2003-01-14
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	YbaB (protein)

Explore in 3D

1J8D \| pdb_00001j8d	Download File View File

Structure Of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Lim, K., Herzberg, O., Structure 2 Function Project (S2F)

(2002) Proteins 46: 393-404

Released	2002-02-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	deoxy-D-mannose-octulosonate 8-phosphate phosphatase (protein)
Unique Ligands	GOL

Explore in 3D

1JOE \| pdb_00001joe	Download File View File

Crystal Structure of Autoinducer-2 Production Protein (LuxS) from Heamophilus influenzae

Chen, C.C.H., Parsons, J.F., Lim, K., Lehmann, C., Tempczyk, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

To be published

Released	2001-08-08
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	AUTOINDUCER-2 PRODUCTION PROTEIN (protein)
Unique Ligands	HG, ZN

Explore in 3D

1K1E \| pdb_00001k1e	Download File View File

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Lim, K., Herzberg, O., Structure 2 Function Project (S2F)

(2002) Proteins 46: 393-404

Released	2002-02-27
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	deoxy-D-mannose-octulosonate 8-phosphate phosphatase (protein)
Unique Ligands	CO, GOL, HG, MES, SO4

Explore in 3D

1KYI \| pdb_00001kyi	Download File View File

HslUV (H. influenzae)-NLVS Vinyl Sulfone Inhibitor Complex

Sousa, M.C., Kessler, B.M., Overkleeft, H.S., McKay, D.B.

(2002) J Mol Biology 318: 779-785

Released	2002-05-15
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	ATP-dependent hsl protease ATP-binding subunit hslU (protein) ATP-dependent protease hslV (protein)
Unique Ligands	ATP, LVS

Explore in 3D

1OFH \| pdb_00001ofh	Download File View File

Asymmetric complex between HslV and I-domain deleted HslU (H. influenzae)

Kwon, A.R., Kessler, B.M., Overkleeft, H.S., McKay, D.B.

(2003) J Mol Biology 330: 185

Released	2003-07-03
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU (protein) ATP-DEPENDENT PROTEASE HSLV (protein)
Unique Ligands	ADP, MG, PO4

Explore in 3D

1OFI \| pdb_00001ofi	Download File View File

Asymmetric complex between HslV and I-domain deleted HslU (H. influenzae)

Kwon, A.R., Kessler, B.M., Overkleeft, H.S., McKay, D.B.

(2003) J Mol Biology 330: 185

Released	2003-07-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU (protein) ATP-DEPENDENT PROTEASE HSLV (protein)
Unique Ligands	ADP, LVS, MG, PO4

Explore in 3D

1PQP \| pdb_00001pqp	Download File View File

Crystal Structure of the C136S Mutant of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae Bound with Aspartate Semialdehyde and Phosphate

Blanco, J., Moore, R.A., Faehnle, C.R., Viola, R.E.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1388-1395

Released	2004-08-10
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Aspartate-semialdehyde dehydrogenase (protein)
Unique Ligands	HSE, PO4

Explore in 3D

1PQU \| pdb_00001pqu	Download File View File

Crystal Structure of the H277N Mutant of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae Bound with NADP, S-methyl cysteine sulfoxide and cacodylate

Blanco, J., Moore, R.A., Viola, R.E.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1388-1395

Released	2004-08-10
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Aspartate-semialdehyde dehydrogenase (protein)
Unique Ligands	CAC, CYS, NAP

Explore in 3D

1Q2X \| pdb_00001q2x	Download File View File

Crystal Structure of the E243D Mutant of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae bound with substrate aspartate semialdehyde

Blanco, J., Moore, R.A., Faehnle, C.R., Coe, D.M., Viola, R.E.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1388-1395

Released	2004-07-27
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Aspartate-semialdehyde dehydrogenase (protein)

Explore in 3D

1Y7L \| pdb_00001y7l	Download File View File

O-Acetylserine Sulfhydrylase Complex

Huang, B., Vetting, M.W., Roderick, S.L.

(2005) J Bacteriol 187: 3201-3205

Released	2005-04-26
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Haemophilus influenzae Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Macromolecule	O-acetylserine sulfhydrylase (protein) decamer fragment of Serine acetyltransferase (protein)
Unique Ligands	SO4

Explore in 3D

2E52 \| pdb_00002e52	Download File View File

Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA at 2.0 angstrom resolution

Watanabe, N., Sato, C., Tanaka, I.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1326-1333

Released	2007-12-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Type II restriction enzyme HindIII (protein) DNA (5'-D(DGPDCPDCPDAPDAPDGPDCPDTPDTPDGPDGPDC)-3') (nucleic acid)
Unique Ligands	ACT, GOL

Explore in 3D

3A4K \| pdb_00003a4k	Download File View File

Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution

Watanabe, N., Sato, C., Takasaki, Y., Tanaka, I.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1326-1333

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Type-2 restriction enzyme HindIII (protein) DNA (5'-D(GPCPCPA)-3') (nucleic acid) DNA (5'-D(GPCPCPAPAPGPCPTPTPGPGPC)-3') (nucleic acid) DNA (5'-D(PAPGPCPTPTPGPGPC)-3') (nucleic acid)
Unique Ligands	ACT, GOL, MG, MN

Explore in 3D

3AXZ \| pdb_00003axz	Download File View File

Crystal structure of Haemophilus influenzae TrmD in complex with adenosine

Yoshida, K., Goto-Ito, S., Ito, T., Hou, Y.M., Yokoyama, S.

(2011) RNA 17: 1236-1246

Released	2011-08-17
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	tRNA (guanine-N(1)-)-methyltransferase (protein)
Unique Ligands	ADN

Explore in 3D

3BJK \| pdb_00003bjk	Download File View File

Crystal structure of HI0827, a hexameric broad specificity acyl-coenzyme A thioesterase: The Asp44Ala mutant enzyme

Willis, M.A., Herzberg, O., Structure 2 Function Project (S2F)

(2008) Biochemistry 47: 2797-2805

Released	2008-02-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Acyl-CoA thioester hydrolase HI0827 (protein)
Unique Ligands	CIT, EDO

Explore in 3D

3CKM \| pdb_00003ckm	Download File View File

LpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A

Vijayalakshmi, J., Saper, M.A.

(2008) Proteins 73: 204-217

Released	2008-05-13
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	YRAM (HI1655) (protein)
Unique Ligands	BME, SO4

Explore in 3D

3ISZ \| pdb_00003isz	Download File View File

Crystal structure of mono-zinc form of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Nocek, B.P., Gillner, D.M., Holz, R.C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

(2010) J Mol Biology 397: 617-626

Released	2009-11-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	SO4, ZN

Explore in 3D

3SF0 \| pdb_00003sf0	Download File View File

Structure of Recombinant Haemophilus Influenzae e(P4) Acid Phosphatase mutant D64N complexed with 5'AMP

Singh, H.

(2011) FEBS J 278: 4374-4381

Released	2011-09-28
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Lipoprotein E (protein)
Unique Ligands	AMP, MG

Explore in 3D

3SWE \| pdb_00003swe	Download File View File

Haemophilus influenzae MurA in complex with UDP-N-acetylmuramic acid and covalent adduct of PEP with Cys117

Zhu, J.-Y., Schonbrunn, E.

(2012) J Biological Chem 287: 12657-12667

Released	2012-03-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	UDP-N-acetylglucosamine 1-carboxyvinyltransferase (protein)
Unique Ligands	EPZ, GOL, SO4

Explore in 3D

3UQ8 \| pdb_00003uq8	Download File View File

Structure of adenylation domain of Haemophilus influenzae DNA ligases bound to NAD+ in adenylated state.

Lahiri, S.D.

(2012) ACS Chem Biol 7: 571-580

Released	2012-01-25
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	DNA ligase (protein)
Unique Ligands	AMP, NAD

Explore in 3D

3WVG \| pdb_00003wvg	Download File View File

Time-Resolved Crystal Structure of HindIII with 0sec soaking

Kawamura, T., Kobayashi, T., Watanabe, N.

(2015) Acta Crystallogr D Biol Crystallogr 71: 256-265

Released	2015-04-08
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Haemophilus influenzae Rd KW20 synthetic construct
Macromolecule	Type-2 restriction enzyme HindIII (protein) DNA (5'-D(GPCPCPAPAPGPCPTPTPGPGPC)-3') (nucleic acid)
Unique Ligands	GOL, NA

1 to 25 of 1,811 Structures

Page 1 of 73

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

CSM Source Database

pLDDT Global Quality Score

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1GQZ | pdb_00001gqz

1IM8 | pdb_00001im8

1J7G | pdb_00001j7g

1J85 | pdb_00001j85

1J8B | pdb_00001j8b

1J8D | pdb_00001j8d

1JOE | pdb_00001joe

1K1E | pdb_00001k1e

1KYI | pdb_00001kyi

1OFH | pdb_00001ofh

1OFI | pdb_00001ofi

1PQP | pdb_00001pqp

1PQU | pdb_00001pqu

1Q2X | pdb_00001q2x

1Y7L | pdb_00001y7l

2E52 | pdb_00002e52

3A4K | pdb_00003a4k

3AXZ | pdb_00003axz

3BJK | pdb_00003bjk

3CKM | pdb_00003ckm

3ISZ | pdb_00003isz

3SF0 | pdb_00003sf0

3SWE | pdb_00003swe

3UQ8 | pdb_00003uq8

3WVG | pdb_00003wvg