MolNFT v1 · #126774 · protein
The structure of the mature HIV-1 ca pentamer in intact virus particles
5MCY · Capsid protein P24: “The structure of the mature HIV-1 ca pentamer in intact virus particles”. Electron microscopy, 20 pockets (best druggability 0.42). MolNFT v1 #126774 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MCY
- Type
- protein
- Length
- 4,420 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P24
- UniProt
- B6DRA0
- Pockets
- 20 · best druggability 0.42
Structure
electron microscopy · 1 distinct chain · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, R, S, T, P, Q, M, N, O, G, d, g, b, e, h, Z, c, f | Capsid protein P24 | protein | 221 | 60% helix, 3% strand | B6DRA0 |
Pockets
20 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.42 | 0.73 | 37 | empty |
| 2 | 195 | 0.41 | 0.73 | 37 | empty |
| 3 | 186 | 0.40 | 0.72 | 32 | empty |
| 4 | 165 | 0.39 | 0.73 | 31 | empty |
| 5 | 159 | 0.37 | 0.72 | 33 | empty |
Interfaces
21 interfaces between chains.
- b–e · 134 Ų buried · 0 hydrogen bonds · protein-protein
- d–g · 130 Ų buried · 0 hydrogen bonds · protein-protein
- Z–c · 129 Ų buried · 0 hydrogen bonds · protein-protein
- R–S · 126 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 125 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MCY · The structure of the mature HIV-1 CA pentamer in intact virus particles · the same entry in another collection · chain A against A, TM-score 1.00
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 B6DRA0
- Elsewhere: RCSB PDB 5MCY · PDBe 5MCY · UniProt B6DRA0
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