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Structure of the native full-length HIV-1 capsid protein in complex with cyclophilin a from helical assembly (-13,7)
Analyse Structure of the native full-length HIV-1 capsid protein in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y9X
- 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.75 | 0.79 | 107 | empty |
| 2 | 825 | 0.74 | 0.78 | 99 | empty |
| 3 | 822 | 0.74 | 0.78 | 87 | empty |
| 4 | 689 | 0.72 | 0.79 | 76 | empty |
| 5 | 631 | 0.70 | 0.78 | 46 | empty |
Interfaces
25 interfaces between chains.
- e–k · 1169 Ų buried · 5 hydrogen bonds · protein-protein
- G–k · 1135 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1131 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1106 Ų buried · 4 hydrogen bonds · protein-protein
- Y–e · 1014 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6Y9X · Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A… · the same entry in another collection · chain N against N, 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 6Y9X · PDBe 6Y9X · UniProt P0C6F2 · UniProt P62937
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