5DT1
Crystal structure of human Fab CAP256-VRC26.25, a potent V1V2-directed HIV-1 broadly neutralizing antibody
- PDB DOI: https://doi.org/10.2210/pdb5DT1/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2015-09-17 Released: 2015-10-21 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.215 
- R-Value Work: 0.169 
- R-Value Observed: 0.172 
wwPDB Validation   3D Report Full Report
This is version 2.2 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 Heavy chain of broadly neutralizing antibody VRC26.25 | A [auth H] | 257 | 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 Light chain of broadly neutralizing antibody VRC26.25 | B [auth L] | 217 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C [auth A] | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
TYS Query on TYS | A [auth H] | L-PEPTIDE LINKING | C9 H11 N O6 S | TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.215 
- R-Value Work: 0.169 
- R-Value Observed: 0.172 
- Space Group: P 21 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 77.016 | α = 90 |
b = 77.027 | β = 90 |
c = 85.227 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHENIX | phasing |
Entry History 
Deposition Data
- Released Date: 2015-10-21  Deposition Author(s): Gorman, J., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2015-10-21
Type: Initial release - Version 1.1: 2015-10-28
Changes: Database references - Version 1.2: 2015-12-30
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary - Version 2.2: 2023-11-15
Changes: Data collection