2I5Y
Crystal structure of CD4M47, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 GP120 envelope glycoprotein and anti-HIV-1 antibody 17B
- PDB DOI: https://doi.org/10.2210/pdb2I5Y/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Human immunodeficiency virus, Homo sapiens, synthetic construct
- Expression System: Drosophila melanogaster, human gammaherpesvirus 4
- Mutation(s): No 
- Deposited: 2006-08-26 Released: 2006-10-10 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.273 
- R-Value Work: 0.214 
- R-Value Observed: 0.214 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Exterior membrane glycoprotein(GP120) | A [auth G], E [auth P] | 313 | Human immunodeficiency virus | 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 | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Antibody 17B Light chain | B [auth L], F [auth Q] | 214 | 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: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Antibody 17B Heavy chain | C [auth H], G [auth R] | 229 | Homo sapiens | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q5EBM2 (Homo sapiens) Explore Q5EBM2  Go to UniProtKB:  Q5EBM2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5EBM2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
CD4M47, SCORPION-TOXIN MIMIC OF CD4 | D [auth M], H [auth S] | 27 | synthetic construct | 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 | I [auth G] J [auth G] K [auth G] L [auth G] M [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
BIF Query on BIF | D [auth M], H [auth S] | L-PEPTIDE LINKING | C15 H15 N O2 | PHE |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.273 
- R-Value Work: 0.214 
- R-Value Observed: 0.214 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 51.437 | α = 90 |
b = 158.16 | β = 93.67 |
c = 109.933 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2006-10-10  Deposition Author(s): Huang, C.-C., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2006-10-10
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2012-06-06
Changes: Structure summary - Version 1.4: 2017-08-16
Changes: Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary