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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Kratch, K.C."

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Search Summary

This query matches 139 Structures.

Refinements

Structure Determination Methodology

experimental (139)

Scientific Name of Source Organism

	Homo sapiens (80)
	Human immunodeficiency virus 1 (64)
	Severe acute respiratory syndrome coronavirus 2 (32)
	HIV-1 06TG.HT008 (9)
	Macaca mulatta (8)
	Mus musculus (6)
	Human immunodeficiency virus (2)
	Lama glama (2)
	Macaca (2)
	HIV-1 M:B_89.6 (1)

More...

Taxonomy

	Riboviria (108)
	Eukaryota (95)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (78)
	ELECTRON MICROSCOPY (52)
	SOLUTION NMR (9)

Polymer Entity Type

Protein (139)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (11)
	2.0 - 2.5 (32)
	2.5 - 3.0 (25)
	3.0 - 3.5 (25)
	3.5 - 4.0 (19)
	4.0 - 4.5 (13)
	> 4.5 (3)

Release Date

	2010 - 2014 (24)
	2015 - 2019 (41)
	2020 - 2024 (74)

Enzyme Classification Name

Hydrolases (3)

Membrane Protein Annotation

	OPM (9)
	MemProtMD (3)
	mpstruc (1)

Symmetry Type

	Asymmetric (112)
	Cyclic (27)

SCOP Classification

	All beta proteins (36)
	Artifacts (4)
	Alpha and beta proteins (a+b) (1)

AllSelected

1 to 25 of 139 Structures

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2ME1 \| pdb_00002me1	Download File View File

HIV-1 gp41 clade B double alanine mutant Membrane Proximal External Region peptide in DPC micelle

Sun, Z.J., Wagner, G., Reinherz, E.L., Kim, M., Song, L., Choi, J., Cheng, Y., Chowdhury, B., Bellot, G., Shih, W.

(2014) J Mol Biology 426: 1095-1108

Released	2013-10-09
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	Gp41 (protein)

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2ME2 \| pdb_00002me2	Download File View File

HIV-1 gp41 clade C Membrane Proximal External Region peptide in DPC micelle

Sun, Z.J., Wagner, G., Reinherz, E.L., Kim, M., Song, L., Choi, J., Cheng, Y., Chowdhury, B., Bellot, G., Shih, W.

(2014) J Mol Biology 426: 1095-1108

Released	2013-10-09
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	Envelope glycoprotein gp160 (protein)

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2ME3 \| pdb_00002me3	Download File View File

HIV-1 gp41 clade C Membrane Proximal External Region peptide in DPC micelle

Sun, Z.J., Wagner, G., Reinherz, E.L., Kim, M., Song, L., Choi, J., Cheng, Y., Chowdhury, B., Bellot, G., Shih, W.

(2014) J Mol Biology 426: 1095-1108

Released	2013-10-09
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	Envelope glycoprotein gp160 (protein)

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2ME4 \| pdb_00002me4	Download File View File

HIV-1 gp41 clade C Membrane Proximal External Region peptide in DPC micelle

Sun, Z.J., Wagner, G., Reinherz, E.L., Kim, M., Song, L., Choi, J., Cheng, Y., Chowdhury, B., Bellot, G., Shih, W.

(2014) J Mol Biology 426: 1095-1108

Released	2013-10-09
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	Envelope glycoprotein gp160 (protein)

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2XRA \| pdb_00002xra	Download File View File

crystal structure of the HK20 Fab in complex with a gp41 mimetic 5- Helix

Sabin, C., Corti, D., Buzon, V., Seaman, M.S., Lutje Hulsik, D., Hinz, A., Vanzetta, F., Agatic, G., Silacci, C., Langedijk, J.P.M., Mainetti, L., Scarlatti, G., Sallusto, F., Weiss, R., Lanzavecchia, A., Weissenhorn, W.

(2010) PLoS Pathog 6: e1001195-e1001195

Released	2010-12-15
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	HK20, HUMAN MONOCLONAL ANTIBODY HEAVY CHAIN (protein) HK20, HUMAN MONOCLONAL ANTIBODY LIGHT CHAIN (protein) TRANSMEMBRANE PROTEIN GP41 (protein)

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3O2D \| pdb_00003o2d	Download File View File

Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody

Freeman, M.M., Seaman, M.S., Rits-Volloch, S., Hong, X., Ho, D.D., Chen, B.

(2010) Structure 18: 1632-1641

Released	2010-12-22
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	T-cell surface glycoprotein CD4 (protein) ibalizumab heavy chain (protein) ibalizumab light chain (protein)

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3RPI \| pdb_00003rpi	Download File View File

Crystal Structure of Fab from 3BNC60, Highly Potent anti-HIV Antibody

Diskin, R., Bjorkman, P.J.

(2011) Science 333: 1633-1637

Released	2011-07-20
Method	X-RAY DIFFRACTION 2.648 Å
Organisms	Homo sapiens
Macromolecule	Heavy chain from highly potent anti-HIV neutralizing antibody (protein) Light chain from highly potent anti-HIV neutralizing antibody (protein)
Unique Ligands	NAG

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3TNM \| pdb_00003tnm	Download File View File

Crystal structure of A32 Fab, an ADCC mediating anti-HIV-1 antibody

Wu, X., Pazgier, M.

(2013) Proc Natl Acad Sci U S A 110: E69-E78

Released	2012-09-26
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain of human anti-HIV-1 Env antibody A32 (protein) Fab light chain of human anti-HIV-1 Env antibody A32 (protein)
Unique Ligands	ACT, CL

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3U7W \| pdb_00003u7w	Download File View File

Crystal structure of NIH45-46 Fab

Diskin, R., Bjorkman, P.J.

(2011) Science 334: 1289-1293

Released	2011-11-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Heavy chain, Ig gamma-1 chain C region (protein) Light chain, Ig kappa chain C region (protein)
Unique Ligands	GOL, NAG, SO4

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3U7Y \| pdb_00003u7y	Download File View File

Structure of NIH45-46 Fab in complex with gp120 of 93TH057 HIV

Diskin, R., Bjorkman, P.J.

(2011) Science 334: 1289-1293

Released	2011-11-16
Method	X-RAY DIFFRACTION 2.4478 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	Envelope glycoprotein gp160 (protein) NIH45-46 heavy chain, Ig gamma-1 chain C region (protein) NIH45-46 light chain, Ig kappa chain C region (protein)
Unique Ligands	CL, FLC, NAG
Unique branched monosaccharides	BMA, MAN, NAG

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4B50 \| pdb_00004b50	Download File View File

Crystal structure of the HIV-1 gp41 MPER-specific llama VHH 2H10

Lutje Hulsik, D., Sabin, C., Macheboeuf, P., Weissenhorn, W.

(2013) PLoS Pathog 9: 3202

Released	2013-03-27
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Lama glama
Macromolecule	2H10 LLAMA VHH (protein)

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4D9L \| pdb_00004d9l	Download File View File

Fab structure of anti-HIV-1 gp120 V2 mAb 697

Pan, R.M., Kong, X.P.

(2012) Virology 427: 198-207

Released	2012-03-21
Method	X-RAY DIFFRACTION 2.485 Å
Organisms	Homo sapiens
Macromolecule	Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697 (protein) Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697 (protein)

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4FQ1 \| pdb_00004fq1	Download File View File

Crystal Structure of PGT121 Fab

Scharf, L., Bjorkman, P.J.

(2012) Proc Natl Acad Sci U S A 109: E3268-E3277

Released	2012-11-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein)
Unique Ligands	NAG

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4FQ2 \| pdb_00004fq2	Download File View File

Crystal Structure of 10-1074 Fab

Scharf, L., Bjorkman, P.J.

(2012) Proc Natl Acad Sci U S A 109: E3268-E3277

Released	2012-11-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein)
Unique Ligands	144, EDO

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4FQC \| pdb_00004fqc	Download File View File

Crystal Structure of PGT121 Fab Bound to a complex-type sialylated N-glycan

Scharf, L., Bjorkman, P.J.

(2012) Proc Natl Acad Sci U S A 109: E3268-E3277

Released	2012-11-14
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein)
Unique Ligands	TAM
Unique branched monosaccharides	BMA, FUC, GAL, MAN, NAG, SIA

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4FQQ \| pdb_00004fqq	Download File View File

Crystal Structure of Germline Antibody PGT121-GL Fab

Scharf, L., Bjorkman, P.J.

(2012) Proc Natl Acad Sci U S A 109: E3268-E3277

Released	2012-11-14
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Homo sapiens
Macromolecule	Fab heavy chain (protein) Fab light chain (protein)
Unique Ligands	NA

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4GW4 \| pdb_00004gw4	Download File View File

Crystal structure of 3BNC60 Fab with P61A mutation

Diskin, R., Fu, B.Z., Bjorkman, P.J.

(2013) Cell 153: 126-138

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	3BNC60 Fab Heavy-chain (protein) 3BNC60 Fab Light-chain (protein)
Unique Ligands	NAG

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4JKP \| pdb_00004jkp	Download File View File

Restricting HIV-1 Pathways for Escape using Rationally-Designed Anti-HIV-1 Antibodies

Diskin, R., Bjorkman, P.J.

(2013) J Exp Medicine 210: 1235-1249

Released	2013-05-15
Method	X-RAY DIFFRACTION 2.82 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	Heavy chain of antibody 45-46M2 (protein) Light chain of antibody 45-46M2 (protein) gp120 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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4JPV \| pdb_00004jpv	Download File View File

Crystal structure of broadly and potently neutralizing antibody 3bnc117 in complex with hiv-1 gp120

Zhou, T., Moquin, S., Kwong, P.D.

(2013) Cell 153: 126-138

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.827 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	HEAVY CHAIN OF ANTIBODY 3BNC117 (protein) HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1 (protein) LIGHT CHAIN OF ANTIBODY 3BNC117 (protein)
Unique Ligands	EDO, EPE, NAG

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4JPW \| pdb_00004jpw	Download File View File

Crystal structure of broadly and potently neutralizing antibody 12a21 in complex with hiv-1 strain 93th057 gp120 mutant

Acharya, P., Luongo, T., Zhou, T., Kwong, P.D.

(2013) Cell 153: 126-138

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.904 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	HEAVY CHAIN OF ANTIBODY 12A21 (protein) HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S (protein) LIGHT CHAIN OF ANTIBODY 12A21 (protein)
Unique Ligands	EPE, NAG

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4NPY \| pdb_00004npy	Download File View File

Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive and potent HIV-1 neutralizing antibody

Julien, J.-P., Diwanji, D.C., Wilson, I.A.

(2013) PLoS Pathog 9: e1003754-e1003754

Released	2013-12-11
Method	X-RAY DIFFRACTION 1.796 Å
Organisms	Homo sapiens
Macromolecule	germline PGT121 heavy chain (protein) germline PGT121 light chain (protein)
Unique Ligands	GOL

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4P9H \| pdb_00004p9h	Download File View File

Crystal structure of 8ANC195 Fab in complex with gp120 of 93TH057 HIV-1 and soluble CD4 D1D2

Scharf, L., Bjorkman, P.J.

(2014) Cell Rep 7: 785-795

Released	2014-05-21
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	Envelope glycoprotein gp160 (protein) Fab heavy chain (protein) Fab light chain (protein) T-cell surface glycoprotein CD4 (protein)
Unique Ligands	BEN, EPE, NAG
Unique branched monosaccharides	BMA, MAN, NAG

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4P9M \| pdb_00004p9m	Download File View File

Crystal structure of 8ANC195 Fab

Scharf, L., Bjorkman, P.J.

(2014) Cell Rep 7: 785-795

Released	2014-05-21
Method	X-RAY DIFFRACTION 2.13 Å
Organisms	Homo sapiens
Macromolecule	8ANC195 Fab heavy chain (protein) 8ANC195 light chain (protein)
Unique Ligands	NAG

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4RQQ \| pdb_00004rqq	Download File View File

Crystal structure of human Fab PGDM1400, a broadly reactive and potent HIV-1 neutralizing antibody

Julien, J.-P., Wilson, I.A.

(2014) Proc Natl Acad Sci U S A 111: 17624-17629

Released	2014-11-19
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	Human anti-HIV-1 antibody PGDM1400 heavy chain (protein) Human anti-HIV-1 antibody PGDM1400 light chain (protein)

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4XMK \| pdb_00004xmk	Download File View File

Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424 in complex with JR-FL V3 peptide

Kong, X.-P., Pan, R.

(2015) J Virol 89: 9090-9102

Released	2015-07-08
Method	X-RAY DIFFRACTION 3.179 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	HIV-1 JR-FL gp120 V3 peptide (protein) Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424 (protein) Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424 (protein)

1 to 25 of 139 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

2ME1 | pdb_00002me1

2ME2 | pdb_00002me2

2ME3 | pdb_00002me3

2ME4 | pdb_00002me4

2XRA | pdb_00002xra

3O2D | pdb_00003o2d

3RPI | pdb_00003rpi

3TNM | pdb_00003tnm

3U7W | pdb_00003u7w

3U7Y | pdb_00003u7y

4B50 | pdb_00004b50

4D9L | pdb_00004d9l

4FQ1 | pdb_00004fq1

4FQ2 | pdb_00004fq2

4FQC | pdb_00004fqc

4FQQ | pdb_00004fqq

4GW4 | pdb_00004gw4

4JKP | pdb_00004jkp

4JPV | pdb_00004jpv

4JPW | pdb_00004jpw

4NPY | pdb_00004npy

4P9H | pdb_00004p9h

4P9M | pdb_00004p9m

4RQQ | pdb_00004rqq

4XMK | pdb_00004xmk