2QSC
Crystal structure analysis of anti-HIV-1 V3-Fab F425-B4e8 in complex with a V3-peptide
- PDB DOI: https://doi.org/10.2210/pdb2QSC/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, Human immunodeficiency virus type 1 group M subtype B (isolate MN)
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2007-07-30 Released: 2008-01-15
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.264
- R-Value Work: 0.219
- R-Value Observed: 0.222
wwPDB Validation 3D Report Full Report
This is version 2.0 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 |
| Fab F425-B4e8, Light chain | A [auth L] | 215 | 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 |
| Fab F425-B4e8, Heavy chain | B [auth H] | 222 | 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: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Envelope glycoprotein gp120 | C [auth P] | 15 | N/A | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN)) Explore P05877 Go to UniProtKB: P05877 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P05877 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | E [auth L], F [auth L], H, I [auth H] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | G [auth L], J [auth H], K [auth H], L [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.264
- R-Value Work: 0.219
- R-Value Observed: 0.222
- Space Group: P 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 82.912 | α = 90 |
| b = 39.858 | β = 108.5 |
| c = 97.96 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2008-01-15 Deposition Author(s): Bell, C.H., Schiefner, A., Stanfield, R.L., Wilson, I.A.
Revision History (Full details and data files)
- Version 1.0: 2008-01-15
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
