5T4Z
STRUCTURE OF THE ANTI-HIV ANTIBODY DH501 THAT BINDS GP120 V3 GLYCAN AND THE BASE OF V3 WITH FREE MAN9 GLYCAN
- PDB DOI: https://doi.org/10.2210/pdb5T4Z/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Macaca mulatta
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2016-08-30 Released: 2017-03-08 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.239 
- R-Value Work: 0.187 
- R-Value Observed: 0.189 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
antibody DH501 Fab heavy chain | A [auth H], C [auth A] | 230 | Macaca mulatta | 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 |
antibody DH501 Fab light chain | B [auth L], D [auth B] | 216 | Macaca mulatta | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CA Query on CA | F [auth H], G [auth L] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.239 
- R-Value Work: 0.187 
- R-Value Observed: 0.189 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 49.757 | α = 90 |
b = 115.997 | β = 97.39 |
c = 76.889 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-03-08  Deposition Author(s): Nicely, N.I., Haynes, B.F.
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: 2017-03-08
Type: Initial release - Version 1.1: 2017-03-15
Changes: Structure summary - Version 1.2: 2017-09-27
Changes: Author supporting evidence - Version 1.3: 2019-12-04
Changes: Author supporting evidence, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary