MolNFT v1 · #170511 · protein
Structure of the native full-length HIV-1 capsid protein in complex with cyclophilin a from helical assembly (-8,13)
6Y9V · Gag-pol polyprotein: “Structure of the native full-length HIV-1 capsid protein in complex with cyclophilin a from helical assembly…”. Electron microscopy, 20 pockets (best druggability 0.75). MolNFT v1 #170511 on GenesisL1: 3D…
- PDB
- 6Y9V
- Type
- protein
- Length
- 2,364 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pol polyprotein; Peptidyl-prolyl cis-trans isomerase a
- EC
- 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-, 5.2.1.8
- UniProt
- P0C6F2, P62937
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 4 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, Y | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 146 | 58% helix, 4% strand | P0C6F2 |
| B, C, D, G, H, d, e, k | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 220 | 55% helix, 2% strand | P0C6F2 |
| J | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 164 | 14% helix, 34% strand | P62937 |
| N, j | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 74 | 61% helix, 0% strand | P0C6F2 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.75 | 0.79 | 83 | empty |
| 2 | 776 | 0.73 | 0.79 | 83 | empty |
| 3 | 767 | 0.73 | 0.78 | 91 | empty |
| 4 | 630 | 0.70 | 0.78 | 48 | empty |
| 5 | 469 | 0.68 | 0.79 | 52 | empty |
Interfaces
22 interfaces between chains.
- G–k · 1154 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1133 Ų buried · 3 hydrogen bonds · protein-protein
- e–k · 1099 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1094 Ų buried · 5 hydrogen bonds · protein-protein
- Y–e · 955 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6Y9V · Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A… · 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 P0C6F2
- Every structure of UniProt P62937
- Elsewhere: RCSB PDB 6Y9V · PDBe 6Y9V · UniProt P0C6F2 · UniProt P62937
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