4OLX
Crystal structure of antibody VRC07-G54L in complex with clade A/E 93TH057 HIV-1 gp120 core
- PDB DOI: https://doi.org/10.2210/pdb4OLX/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Human immunodeficiency virus 1, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2014-01-25 Released: 2014-09-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.247
- R-Value Work: 0.201
- R-Value Observed: 0.203
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 |
| Envelope glycoprotein gp160 | A [auth G] | 353 | Human immunodeficiency virus 1 | Mutation(s): 0 Gene Names: Env, pol |  |
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 |
| Antigen binding fragment of heavy chain: Antibody VRC01 | B [auth H] | 228 | Homo sapiens | Mutation(s): 0 Gene Names: Heavy chain |  |
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 |
| Antigen binding fragment of light chain: Antibody VRC01 | C [auth L] | 210 | Homo sapiens | Mutation(s): 0 Gene Names: Light chain |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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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: 2.20 Å
- R-Value Free: 0.247
- R-Value Work: 0.201
- R-Value Observed: 0.203
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.442 | α = 90 |
| b = 76.036 | β = 90 |
| c = 198.158 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| PHASES | phasing |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2014-09-03 Deposition Author(s): Kwon, Y.D., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2014-09-03
Type: Initial release - Version 1.1: 2014-10-22
Changes: Database references - Version 1.2: 2017-08-23
Changes: Refinement description, Source and taxonomy - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2021-06-02
Changes: Source and taxonomy, Structure summary - Version 1.5: 2023-09-20
Changes: Data collection, Database references, Refinement description
