MolNFT v1 · #73450 · protein
Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody
3O2D · Ibalizumab light chain: “Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody”. X-ray diffraction, 7 pockets (best druggability 0.64). MolNFT v1 #73450 on GenesisL1: 3D structure, binding sites…
- PDB
- 3O2D
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ibalizumab light chain; Ibalizumab heavy chain; T-cell surface glycoprotein CD4
- UniProt
- P01730
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Ibalizumab light chain | protein | 216 | 6% helix, 53% strand | — |
| H | Ibalizumab heavy chain | protein | 222 | 8% helix, 52% strand | — |
| A | T-cell surface glycoprotein CD4 | protein | 178 | 8% helix, 53% strand | P01730 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.64 | 0.74 | 68 | empty |
| 2 | 125 | 0.53 | 0.81 | 24 | empty |
| 3 | 123 | 0.52 | 0.81 | 20 | empty |
| 4 | 64 | 0.51 | 0.86 | 15 | empty |
| 5 | 83 | 0.42 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1854 Ų buried · 19 hydrogen bonds · protein-protein
- H–A · 752 Ų buried · 12 hydrogen bonds · protein-protein
- L–A · 565 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3O2D · Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral… · the same entry in another collection · chain L against L, TM-score 1.00
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 3O2D · PDBe 3O2D · UniProt P01730
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