RCSB Protein Data Bank - RCSB PDB - 3IDY Structure Summary

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Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C2221

DOI:10.2210/pdb3idy/pdb

3IDY

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Primary Citation

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Molecular Description

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Classification:	Immune System
Structure Weight:	173444.94

Molecule:

HIV-1 HxBc2 gp120 core

Polymer:

Type:

protein

Length:

317

Chains:

A, G

Mutation:

M95W, T257S, S375W, A443M, W96C, V275C, I109C, Q428C

Organism

Human immunodeficiency virus 1

Gene Name

env

UniProtKB:

| | P04578

Molecule:

Fab b13 heavy chain

Polymer:

Type:

protein

Length:

231

Chains:

B, H

Organism

Homo sapiens

Molecule:

Fab b13 light chain

Polymer:

Type:

protein

Length:

215

Chains:

C, L

Organism

Homo sapiens

Source

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Polymer: 1

Scientific Name:

Human immunodeficiency virus 1

Taxonomy

Expression System:

Homo sapiens

Polymer: 2

Scientific Name:

Homo sapiens

Taxonomy

Common Name:

Human

Expression System:

Homo sapiens

Polymer: 3

Scientific Name:

Homo sapiens

Taxonomy

Common Name:

Human

Expression System:

Homo sapiens

Related PDB Entries

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Identifier	Details
3IDX	Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13. in space group C222

Ligand Chemical Component

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Identifier	Formula	Name	Interactions
NAG Search Download	C₈ H₁₅ N O₆	N-ACETYL-D-GLUCOSAMINE		Ligand Explorer
SO4 Search Download	O₄ S	SULFATE ION		Ligand Explorer

External Domain Annotations Hide
CATH Classification v3.4.0: 6 Domains - data from CATH

Pfam Classification: 14 Domains - data from Pfam
Structural Biology Knowledgebase Data Hide

Data in orange boxes are gathered from external resources (when available).

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Biological Assembly 1

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Biological assembly 1 assigned by authors

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Deposition Summary

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Authors: Chen, L., Kwon, Y.D., Zhou, T., Wu, X., O'Dell, S., Cavacini, L., Hessell, A.J., Pancera, M., Tang, M., Xu, L., Yang, Z.Y., Zhang, M.Y., Arthos, J., Burton, D.R., Dimitrov, D.S., Nabel, G.J., Posner, M., Sodroski, J., Wyatt, R., Mascola, J.R., Kwong, P.D.

Deposition:	2009-07-22
Release:	2009-11-17
Last Modified (REVDAT):	2011-07-13

Revision History Hide

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2011-07-13
Non-polymer description

2011-07-13
Version format compliance

Experimental Details

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Method: X-RAY DIFFRACTION
Exp. Data:
Structure Factors
EDS

Unit Cell:
	Length [Å]	Angles [°]
	a = 106.17	α = 90.00
	b = 204.32	β = 90.00
	c = 216.89	γ = 90.00

Molecule of the Month Hide
Epidermal Growth Factor

Nanobodies

Antibodies

Hemagglutinin