5UKR
Structure of unliganded anti-gp120 CD4bs antibody DH522.2 Fab in complex with a gp120 core
- PDB DOI: https://doi.org/10.2210/pdb5UKR/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Macaca mulatta, Human immunodeficiency virus 1
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2017-01-23 Released: 2017-12-06
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Duke University Center for AIDS Research
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.71 Å
- R-Value Free: 0.265
- R-Value Work: 0.201
- R-Value Observed: 0.206
This is version 1.3 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 |
| DH522.2 Fab fragment heavy chain | A [auth H] | 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 |
| DH522.2 Fab fragment light chain | B [auth L] | 216 | 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: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chimeric B.YU2 gp120 core derived from HIV-1 Env | C [auth G] | 313 | Human immunodeficiency virus 1 | Mutation(s): 0 |  |
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: 2.71 Å
- R-Value Free: 0.265
- R-Value Work: 0.201
- R-Value Observed: 0.206
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.851 | α = 90 |
| b = 71.973 | β = 90 |
| c = 252.228 | 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: 2017-12-06 Deposition Author(s): Nicely, N.I.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | UM1-AI100645 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01-AI087202 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01-AI118571 |
| Duke University Center for AIDS Research | United States | P30-AI-64518 |
Revision History (Full details and data files)
- Version 1.0: 2017-12-06
Type: Initial release - Version 1.1: 2019-12-11
Changes: Author supporting evidence - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
