4YE4
Crystal Structure of Neutralizing Antibody HJ16 in Complex with HIV-1 gp120
- PDB DOI: https://doi.org/10.2210/pdb4YE4/pdb
- Classification: Viral protein/Immune system
- Organism(s): Human immunodeficiency virus, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2015-02-23 Released: 2015-07-22
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.72 Å
- R-Value Free: 0.242
- R-Value Work: 0.187
- R-Value Observed: 0.190
This is version 1.5 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 |
| HT593.1 gp120 | A [auth G] | 356 | Human immunodeficiency virus | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for Q69994 (Human immunodeficiency virus 1) Explore Q69994 Go to UniProtKB: Q69994 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q69994 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Heavy chain human antibody HJ16 | B [auth H] | 228 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Light chain of HJ16 | C [auth L] | 218 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 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: 2.72 Å
- R-Value Free: 0.242
- R-Value Work: 0.187
- R-Value Observed: 0.190
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 87.712 | α = 90 |
| b = 99.037 | β = 90 |
| c = 180.426 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-07-22 Deposition Author(s): Kwong, P.D., Chen, L., Zhou, T.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2015-07-22
Type: Initial release - Version 1.1: 2015-10-07
Changes: Experimental preparation - Version 1.2: 2017-09-13
Changes: Author supporting evidence, Derived calculations - Version 1.3: 2020-03-04
Changes: Data collection, Database references - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2022-03-30
Changes: Author supporting evidence, Database references, Structure summary
