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 
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 
This is version 2.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
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 AnnotationsExpand | |||||
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Oligosaccharides
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 | ||
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 | E [auth G] F [auth G] G H [auth G] I [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
PEG Query on PEG | X [auth G], Y [auth G] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
SO4 Query on SO4 | HA [auth L], Q [auth G], R [auth G] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
EDO Query on EDO | BA [auth H] CA [auth H] DA [auth H] EA [auth H] FA [auth H] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
NA Query on NA | AA [auth G], GA [auth H], Z [auth G] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
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 Name | Purpose |
---|---|
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |
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