4LSQ
Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057 with LOOP D and Loop V5 from clade A strain 3415_v1_c1
- PDB DOI: https://doi.org/10.2210/pdb4LSQ/pdb
- Classification: viral protein/immune system
- Organism(s): Human immunodeficiency virus 1, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2013-07-23 Released: 2013-08-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.229
- R-Value Work: 0.192
- R-Value Observed: 0.194
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 GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1 | A [auth G] | 352 | Human immunodeficiency virus 1 | Mutation(s): 0 Gene Names: env |  |
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 |
| HEAVY CHAIN OF ANTIBODY VRC-CH31 | B [auth H] | 236 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| LIGHT CHAIN OF ANTIBODY VRC-CH31 WITH N70D MUTATION | C [auth L] | 210 | Homo sapiens | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 5 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 |  | ||
| CD Query on CD | M [auth G], N [auth G], U [auth H], V [auth H], Y [auth L] | CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N |  | ||
| BU3 Query on BU3 | O [auth G] | (R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N |  | ||
| CL Query on CL | P [auth G], W [auth H], X [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | Q [auth G], R [auth G], S [auth G], T [auth G] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.229
- R-Value Work: 0.192
- R-Value Observed: 0.194
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.514 | α = 90 |
| b = 67.621 | β = 90 |
| c = 221.088 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
Entry History
Deposition Data
- Released Date: 2013-08-21 Deposition Author(s): Zhou, T., Moquin, S., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2013-08-21
Type: Initial release - Version 1.1: 2013-09-04
Changes: Database references - Version 1.2: 2013-09-25
Changes: Database references - Version 1.3: 2014-05-07
Changes: Other - Version 1.4: 2017-11-15
Changes: Refinement description - Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
