4LAJ
Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4
- PDB DOI: https://doi.org/10.2210/pdb4LAJ/pdb
- Classification: VIRAL PROTEIN/INHIBITOR
- Organism(s): Human immunodeficiency virus 1, Lama glama
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2013-06-20 Released: 2013-08-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.14 Å
- R-Value Free: 0.227 
- R-Value Work: 0.185 
- R-Value Observed: 0.188 
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 |
HIV-1 YU2 gp120 envelope glycoprotein | A [auth J], B [auth F], C [auth A], D [auth B] | 376 | Human immunodeficiency virus 1 | Mutation(s): 0  Gene Names: Env | |
UniProt | |||||
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)) Explore P35961  Go to UniProtKB:  P35961 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P35961 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
CD4-mimetic miniprotein M48U1 | E [auth K], F [auth D], G, H [auth C] | 28 | N/A | 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 |
Llama single domain antibody, JM4 | I [auth H], J [auth M], K [auth L], L [auth I] | 129 | Lama glama | Mutation(s): 0  | |
UniProt | |||||
Find proteins for A2KD57 (Lama glama) Explore A2KD57  Go to UniProtKB:  A2KD57 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A2KD57 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth F] BA [auth F] CA [auth F] DA [auth F] EA [auth F] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ACA Query on ACA | CB [auth B] | 6-AMINOHEXANOIC ACID C6 H13 N O2 SLXKOJJOQWFEFD-UHFFFAOYSA-N | |||
EDO Query on EDO | AB [auth B] BB [auth B] OA [auth A] PA [auth A] QA [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
U2X Query on U2X | E [auth K], F [auth D], G, H [auth C] | L-PEPTIDE LINKING | C16 H23 N O3 | TYR |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_001094 Query on PRD_001094 | E [auth C], F [auth D], G, H [auth K] | CD4-MIMETIC MINIPROTEIN M48U1 | Peptide-like / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.14 Å
- R-Value Free: 0.227 
- R-Value Work: 0.185 
- R-Value Observed: 0.188 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 96.772 | α = 90 |
b = 86.221 | β = 102.88 |
c = 144.848 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-08-14  Deposition Author(s): Acharya, P., Luongo, T.S., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2013-08-14
Type: Initial release - Version 1.1: 2013-08-21
Changes: Structure summary - Version 1.2: 2013-09-04
Changes: Database references - Version 1.3: 2014-04-09
Changes: Source and taxonomy - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.5: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary - Version 2.0: 2023-11-15
Changes: Atomic model, Data collection