5TE7
Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade C Strain DU172.17 gp120 Core
- PDB DOI: https://doi.org/10.2210/pdb5TE7/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, Human immunodeficiency virus 1
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2016-09-20 Released: 2016-11-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.228
- R-Value Work: 0.190
- R-Value Observed: 0.191
This is version 1.4 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Heavy chain of N6 | A [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: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Light chain of N6 | B [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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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| HIV-1 gp120 core | C [auth G] | 350 | Human immunodeficiency virus 1 | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for Q202J8 (Human immunodeficiency virus 1) Explore Q202J8 Go to UniProtKB: Q202J8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q202J8 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | D [auth H], R [auth G] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| NAG Query on NAG | G [auth L] K [auth G] L [auth G] M [auth G] N [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| EDO Query on EDO | E [auth H] F [auth H] H [auth L] I [auth L] J [auth L] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.228
- R-Value Work: 0.190
- R-Value Observed: 0.191
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 62.675 | α = 90 |
| b = 65.547 | β = 90 |
| c = 241.522 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| 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 - Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
