MolNFT v1 · #103204 · protein
Crystal structure of 8ANC195 Fab in complex with GP120 of 93TH057 HIV- 1 and soluble CD4 D1D2
4P9H · T-cell surface glycoprotein CD4: “Crystal structure of 8ANC195 Fab in complex with GP120 of 93TH057 HIV- 1 and soluble CD4 D1D2”. X-ray diffraction, 4 ligands (BEN, NAG, MAN), 9 pockets (best druggability 0.71). MolNFT v1 #103204 on…
- PDB
- 4P9H
- Type
- protein
- Length
- 932 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD4; Envelope glycoprotein GP160; Fab heavy chain; Fab light…
- UniProt
- P01730, Q0ED31
- Ligands
- BEN, NAG, MAN, BMA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | T-cell surface glycoprotein CD4 | protein | 167 | 2% helix, 50% strand | P01730 |
| G | Envelope glycoprotein GP160 | protein | 338 | 17% helix, 37% strand | Q0ED31 |
| H | Fab heavy chain | protein | 215 | 6% helix, 51% strand | — |
| L | Fab light chain | protein | 212 | 7% helix, 50% strand | — |
Ligands and binding sites
- BEN · Benzamidine · ligand · 2 copies · chains G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains C, G, H
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains H, G
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.71 | 0.97 | 25 | empty |
| 2 | 655 | 0.69 | 0.77 | 83 | NAG |
| 3 | 79 | 0.53 | 0.85 | 19 | NAG |
| 4 | 279 | 0.50 | 0.74 | 39 | empty |
| 5 | 94 | 0.48 | 0.81 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1736 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 981 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 728 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4P9H · Crystal structure of 8ANC195 Fab in complex with gp120 of 93TH057 HIV-1 and soluble CD4… · the same entry in another collection · chain C against C, 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 C against A, TM-score 0.95
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
- Every structure of UniProt Q0ED31
- Elsewhere: RCSB PDB 4P9H · PDBe 4P9H · UniProt P01730 · UniProt Q0ED31
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