5TE6
Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade AE Strain 93TH057 gp120 Core
- PDB DOI: https://doi.org/10.2210/pdb5TE6/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Human immunodeficiency virus 1, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2016-09-20 Released: 2016-11-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.278 
- R-Value Work: 0.227 
- R-Value Observed: 0.229 
This is version 1.3 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 |
clade A/E 93TH057 HIV-1 gp120 core | A [auth G] | 353 | Human immunodeficiency virus 1 | Mutation(s): 0  Gene Names: HIV-1 Env | |
UniProt | |||||
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1) Explore A0A0M3KKW9  Go to UniProtKB:  A0A0M3KKW9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A0M3KKW9 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Heavy chain of N6 | B [auth H] | 225 | 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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Light chain of N6 | 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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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
EPE Query on EPE | N [auth G] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N | |||
NAG Query on NAG | D [auth G] E [auth G] F [auth G] G H [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.278 
- R-Value Work: 0.227 
- R-Value Observed: 0.229 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 64.692 | α = 90 |
b = 65.822 | β = 90 |
c = 238.012 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
Coot | model building |
Entry History 
Deposition Data
- Released Date: 2016-11-16  Deposition Author(s): Zhou, T., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2016-11-16
Type: Initial release - Version 1.1: 2016-11-23
Changes: Database references, Structure summary - Version 1.2: 2016-11-30
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary