4LSP

Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057

PDB DOI: https://doi.org/10.2210/pdb4LSP/pdb

Classification: viral protein/immune system
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2013-07-23 Released: 2013-09-04
Deposition Author(s): Zhou, T., Moquin, S., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.214
R-Value Work: 0.180
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 92.13 kDa
Atom Count: 6,498
Modelled Residue Count: 771
Deposited Residue Count: 799
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 CLADE A/E STRAIN 93TH057 GP120	A [auth G]	353	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1) Explore Q0ED31 Go to UniProtKB: Q0ED31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0ED31
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAVY CHAIN OF ANTIBODY VRC-CH31	B [auth H]	236	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN OF ANTIBODY VRC-CH31	C [auth L]	210	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	3		N-Glycosylation	Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth G] SDF format, chain F [auth G] SDF format, chain G SDF format, chain H [auth G] SDF format, chain I [auth G] SDF format, chain J [auth G] SDF format, chain K [auth G] SDF format, chain L [auth G] SDF format, chain M [auth G] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain P [auth G] MOL2 format, chain E [auth G] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain H [auth G] MOL2 format, chain I [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G]	E [auth G] F [auth G] G H [auth G] I [auth G] E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G], O [auth G], P [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Interactions & Density Focus chain E [auth G] Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain X [auth G] SDF format, chain Y [auth G] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G]	X [auth G], Y [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain X [auth G] Focus chain Y [auth G] Interactions & Density Focus chain X [auth G] Focus chain Y [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain HA [auth L] SDF format, chain Q [auth G] SDF format, chain R [auth G] MOL2 format, chain HA [auth L] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth G]	HA [auth L], Q [auth G], R [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HA [auth L] Focus chain Q [auth G] Focus chain R [auth G] Interactions & Density Focus chain HA [auth L] Focus chain Q [auth G] Focus chain R [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain CA [auth H] SDF format, chain DA [auth H] SDF format, chain EA [auth H] SDF format, chain FA [auth H] SDF format, chain IA [auth L] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain IA [auth L] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G]	BA [auth H] CA [auth H] DA [auth H] EA [auth H] FA [auth H] BA [auth H], CA [auth H], DA [auth H], EA [auth H], FA [auth H], IA [auth L], S [auth G], T [auth G], U [auth G], V [auth G], W [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain IA [auth L] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain IA [auth L] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain GA [auth H] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain Z [auth G]	AA [auth G], GA [auth H], Z [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain GA [auth H] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain GA [auth H] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.214
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.392	α = 90
b = 83.958	β = 90
c = 175.734	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Zhou, T.

Moquin, S.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2013-09-25
Changes: Database references
Version 1.2: 2014-05-07
Changes: Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-06-02
Changes: Source and taxonomy, Structure summary
Version 2.2: 2023-09-20
Changes: Data collection, Database references, Refinement description