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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 182 Structures.

Refinements

Structure Determination Methodology

experimental (182)

Scientific Name of Source Organism

	Homo sapiens (104)
	synthetic construct (58)
	unidentified (10)
	Corynebacterium ammoniagenes (6)
	Mentha x piperita (4)
	Saccharomyces cerevisiae S288C (4)
	Trichomonas vaginalis G3 (4)
	Arabidopsis thaliana (3)
	Bacillus subtilis (3)
	Foot-and-mouth disease virus C-S8c1 (3)

More...

Taxonomy

	Eukaryota (135)
	other sequences (58)
	Bacteria (33)
	unclassified sequences (10)
	Archaea (7)
	Riboviria (4)
	Varidnaviria (2)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (181)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (182)
	DNA (108)
	RNA (8)
	NA-hybrid (2)

Refinement Resolution (Å)

	1.0 - 1.5 (10)
	1.5 - 2.0 (89)
	2.0 - 2.5 (52)
	2.5 - 3.0 (21)
	3.0 - 3.5 (10)

Release Date

	2005 - 2009 (17)
	2010 - 2014 (30)
	2015 - 2019 (61)
	2020 - 2024 (74)

Enzyme Classification Name

	Transferases (147)
	Lyases (73)
	Hydrolases (11)
	Ligases (3)
	Oxidoreductases (2)

Membrane Protein Annotation

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

Symmetry Type

	Asymmetric (142)
	Cyclic (34)
	Dihedral (15)

SCOP Classification

	All alpha proteins (28)
	Alpha and beta proteins (a+b) (25)
	Artifacts (11)
	Alpha and beta proteins (a/b) (7)
	Membrane and cell surface proteins and peptides (1)
	All beta proteins (2)
	Multi-domain proteins (alpha and beta) (3)

AllSelected

1 to 25 of 182 Structures

Page 1 of 8

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1XSP \| pdb_00001xsp	Download File View File

Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C.

(2005) Nat Struct Mol Biol 12: 97-98

Released	2005-01-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPAPCPG)-3' (nucleic acid) 5'-D(CPGPGPCPCPGPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCPG)-3' (nucleic acid)
Unique Ligands	NA, PPV

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2BCQ \| pdb_00002bcq	Download File View File

DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Pedersen, L.C., Kunkel, T.A.

(2006) Cell 124: 331-342

Released	2006-03-07
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPAPCPG)-3' (nucleic acid) 5'-D(CPGPGPCPCPGPTPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCP*G)-3' (nucleic acid)
Unique Ligands	EDO, MG, NA, PPV

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2BCR \| pdb_00002bcr	Download File View File

DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Pedersen, L.C., Kunkel, T.A.

(2006) Cell 124: 331-342

Released	2006-03-07
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPAPCPG)-3' (nucleic acid) 5'-D(CPGPGPCPCPGPAPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCP*G)-3' (nucleic acid)
Unique Ligands	EDO, MG, NA, PPV

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2BCS \| pdb_00002bcs	Download File View File

DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dcmp

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Pedersen, L.C., Kunkel, T.A.

(2006) Cell 124: 331-342

Released	2006-03-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPAPCPG)-3' (nucleic acid) 5'-D(CPGPGPCPCPGPCPTPAPCPTPG)-3' (nucleic acid) 5'-D(GPCPCP*G)-3' (nucleic acid)
Unique Ligands	MG, NA, PPV

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2BCU \| pdb_00002bcu	Download File View File

DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp and a T:T mismatch

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Pedersen, L.C., Kunkel, T.A.

(2006) Cell 124: 331-342

Released	2006-03-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) 5'-D(CPAPGPTPTPCPG)-3' (nucleic acid) 5'-D(CPGPGPCPCPGPAPTPAPCPTPG)-3' (nucleic acid) 5'-D(PGPCPCP*G)-3' (nucleic acid)
Unique Ligands	NA, PPV

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2E90 \| pdb_00002e90	Download File View File

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium, pyrophosphate and FPP

Guo, R.T., Ko, T.P., Chen, C.K.-M., Jeng, W.Y., Chang, T.H., Liang, P.H., Oldfield, E., Wang, A.H.-J.

(2007) Proc Natl Acad Sci U S A 104: 10022-10027

Released	2007-06-12
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Geranylgeranyl pyrophosphate synthetase (protein)
Unique Ligands	FPP, MG, PPV

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2E9T \| pdb_00002e9t	Download File View File

Foot-and-mouth disease virus RNA-polymerase RNA dependent in complex with a template-primer RNA and 5F-UTP

Ferrer-Orta, C., Arias, A., Perez-Luque, R., Escarmis, C., Domingo, E., Verdaguer, N.

(2007) Proc Natl Acad Sci U S A 104: 9463-9468

Released	2007-06-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Foot-and-mouth disease virus C-S8c1
Macromolecule	RNA-dependent RNA polymerase (protein) 5'-R(GPGPGPCPCPCP(5FU))-3' (nucleic acid) 5'-R(PUPAPGPGPGPCPCP*C)-3' (nucleic acid)
Unique Ligands	MG, PPV

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2E9Z \| pdb_00002e9z	Download File View File

Foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, ATP and UTP

Ferrer-Orta, C., Arias, A., Perez-Luque, R., Escarmis, C., Domingo, E., Verdaguer, N.

(2007) Proc Natl Acad Sci U S A 104: 9463-9468

Released	2007-06-26
Method	X-RAY DIFFRACTION 3 Å
Organisms	Foot-and-mouth disease virus C-S8c1
Macromolecule	RNA-dependent RNA polymerase (protein) 5'-R(CPAPUPGPGPGPCPCPC)-3' (nucleic acid) 5'-R(GPGPGPCPCPCPA)-3' (nucleic acid)
Unique Ligands	MG, PPV, UTP

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2EC0 \| pdb_00002ec0	Download File View File

RNA-dependent RNA polymerase of foot-and-mouth disease virus in complex with a template-primer RNA and ATP

Ferrer-Orta, C., Arias, A., Perez-Luque, R., Escarmis, C., Domingo, E., Verdaguer, N.

(2007) Proc Natl Acad Sci U S A 104: 9463-9468

Released	2007-06-26
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Foot-and-mouth disease virus C-S8c1
Macromolecule	RNA-dependent RNA polymerase (protein) 5'-R(GPGPGPCPCPCPA)-3' (nucleic acid) 5'-R(PAPUPGPGPGPCPCP*C)-3' (nucleic acid)
Unique Ligands	MG, PPV

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2O1C \| pdb_00002o1c	Download File View File

Structure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase

Gabelli, S.B., Bianchet, M.A., Amzel, L.M.

(2007) Structure 15: 1014-1022

Released	2007-08-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	dATP pyrophosphohydrolase (protein)
Unique Ligands	PPV, SO4

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2O5W \| pdb_00002o5w	Download File View File

Structure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase in complex with Sm+3 and pyrophosphate

Gabelli, S.B., Bianchet, M.A., Amzel, L.M.

(2007) Structure 15: 1014-1022

Released	2007-08-28
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia coli
Macromolecule	dATP pyrophosphohydrolase (protein)
Unique Ligands	NA, PPV, SM, SO4

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2PFQ \| pdb_00002pfq	Download File View File

Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal

Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Pedersen, L.C., Kunkel, T.A.

(2007) DNA Repair (Amst) 6: 1333-1340

Released	2007-05-15
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) Downstream Primer (nucleic acid) Primer (nucleic acid) Template (nucleic acid)
Unique Ligands	DCP, MG, MN, NA, PPV

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2PMD \| pdb_00002pmd	Download File View File

The structures of aIF2gamma subunit from the archaeon Sulfolobus solfataricus in the GDP-bound form.

Nikonov, O.S., Stolboushkina, E.A., Nikulin, A.D., Hasenohrl, D., Blaesi, U., Manstein, D.J., Fedorov, R.V., Garber, M.B., Nikonov, S.V.

(2007) J Mol Biology 373: 328-336

Released	2007-11-06
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Translation initiation factor 2 gamma subunit (protein)
Unique Ligands	GDP, GNP, PPV

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2X0K \| pdb_00002x0k	Download File View File

Crystal structure of modular FAD synthetase from Corynebacterium ammoniagenes

Herguedas, B., Hermoso, J.A., Martinez-Julvez, M., Medina, M., Frago, S.

(2010) J Mol Biology 400: 218

Released	2010-05-26
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Corynebacterium ammoniagenes
Macromolecule	RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF (protein)
Unique Ligands	PPV, SO4

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3AQ0 \| pdb_00003aq0	Download File View File

Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant)

Hsieh, F.-L., Chang, T.-H., Ko, T.-P., Wang, A.H.-J.

(2011) Plant Physiol 155: 1079-1090

Released	2011-01-19
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Arabidopsis thaliana
Macromolecule	Geranyl diphosphate synthase (protein)
Unique Ligands	FPP, ISY, MG, PEG, PPV

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3ATR \| pdb_00003atr	Download File View File

Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius co-crystallized with its ligand

Fujihashi, M., Sasaki, D., Iwata, Y., Yoshimura, T., Hemmi, H., Miki, K.

(2011) J Mol Biology 409: 543-557

Released	2011-05-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Sulfolobus acidocaldarius
Macromolecule	Conserved Archaeal protein (protein)
Unique Ligands	DD9, FDA, PPV

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3EPH \| pdb_00003eph	Download File View File

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

Huang, R.H., Zhou, C.

(2008) Proc Natl Acad Sci U S A 105: 16142-16147

Released	2008-11-04
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	tRNA isopentenyltransferase (protein) tRNA (nucleic acid)
Unique Ligands	MG, PPV, ZN

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3EPK \| pdb_00003epk	Download File View File

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

Huang, R.H., Zhou, C.

(2008) Proc Natl Acad Sci U S A 105: 16142-16147

Released	2008-11-04
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	tRNA isopentenyltransferase (protein) tRNA (nucleic acid)
Unique Ligands	DST, MG, PPV, ZN

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3H2B \| pdb_00003h2b	Download File View File

Crystal structure of the SAM-dependent methyltransferase cg3271 from Corynebacterium glutamicum in complex with S-adenosyl-L-homocysteine and pyrophosphate. Northeast Structural Genomics Consortium Target CgR113A

Forouhar, F., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Foote, E.L., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

To be published

Released	2009-04-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Corynebacterium glutamicum ATCC 13032
Macromolecule	SAM-dependent methyltransferase (protein)
Unique Ligands	PPV, SAH

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3JYY \| pdb_00003jyy	Download File View File

SeMet LinB complexed with PPi

Morar, M., Wright, G.D.

(2009) Structure 17: 1649-1659

Released	2009-11-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Enterococcus faecium
Macromolecule	Lincosamide nucleotidyltransferase (protein)
Unique Ligands	MG, PPV

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3KRF \| pdb_00003krf	Download File View File

Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium, IPP, and DMASPP (I)

Chang, T.-H., Hsieh, F.-L., Ko, T.-P., Wang, A.H.-J.

(2010) Plant Cell 22: 454-467

Released	2010-02-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Mentha x piperita
Macromolecule	Geranyl diphosphate synthase large subunit (protein) Geranyl diphosphate synthase small subunit (protein)
Unique Ligands	DST, EDO, IPE, MG, PPV

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3KRO \| pdb_00003kro	Download File View File

Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium, IPP, and DMASPP (II)

Chang, T.-H., Hsieh, F.-L., Ko, T.-P., Wang, A.H.-J.

(2010) Plant Cell 22: 454-467

Released	2010-02-23
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Mentha x piperita
Macromolecule	Geranyl diphosphate synthase large subunit (protein) Geranyl diphosphate synthase small subunit (protein)
Unique Ligands	DST, EDO, IPE, MG, PPV

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3KRP \| pdb_00003krp	Download File View File

Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium and GPP

Chang, T.-H., Hsieh, F.-L., Ko, T.-P., Wang, A.H.-J.

(2010) Plant Cell 22: 454-467

Released	2010-02-23
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Mentha x piperita
Macromolecule	Geranyl diphosphate synthase large subunit (protein) Geranyl diphosphate synthase small subunit (protein)
Unique Ligands	EDO, GPP, MG, PPV

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3MDA \| pdb_00003mda	Download File View File

DNA polymerase lambda in complex with araC

Garcia-Diaz, M., Murray, M., Kunkel, T., Chou, K.M.

(2010) J Biological Chem 285: 16874-16879

Released	2010-04-28
Method	X-RAY DIFFRACTION 2.031 Å
Organisms	Homo sapiens
Macromolecule	DNA polymerase lambda (protein) DNA (5'-D(CPAPGPTPAPCP(CAR))-3') (nucleic acid) DNA (5'-D(CPGPGPCPGPGPTPAPCPTPG)-3') (nucleic acid) DNA (5'-D(PGPCPCPG)-3') (nucleic acid)
Unique Ligands	MG, NA, PPV

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3NPK \| pdb_00003npk	Download File View File

The crystal structure of geranyltranstransferase from Campylobacter jejuni

Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2010-07-14
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Campylobacter jejuni RM1221
Macromolecule	Geranyltranstransferase (protein)
Unique Ligands	GOL, PPV

1 to 25 of 182 Structures

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Structure Determination Methodology

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

1XSP | pdb_00001xsp

2BCQ | pdb_00002bcq

2BCR | pdb_00002bcr

2BCS | pdb_00002bcs

2BCU | pdb_00002bcu

2E90 | pdb_00002e90

2E9T | pdb_00002e9t

2E9Z | pdb_00002e9z

2EC0 | pdb_00002ec0

2O1C | pdb_00002o1c

2O5W | pdb_00002o5w

2PFQ | pdb_00002pfq

2PMD | pdb_00002pmd

2X0K | pdb_00002x0k

3AQ0 | pdb_00003aq0

3ATR | pdb_00003atr

3EPH | pdb_00003eph

3EPK | pdb_00003epk

3H2B | pdb_00003h2b

3JYY | pdb_00003jyy

3KRF | pdb_00003krf

3KRO | pdb_00003kro

3KRP | pdb_00003krp

3MDA | pdb_00003mda

3NPK | pdb_00003npk