Research workbench
Structure of the native full-length HIV-1 capsid protein in complex with cyclophilin a from helical assembly (-13,10)
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
- 6ZDJ
- Type
- protein
- Length
- 2,364 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag protein; Peptidyl-prolyl cis-trans isomerase a
- EC
- 5.2.1.8
- UniProt
- Q71B31, P62937
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 4 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, Y | Gag protein | protein | 146 | 58% helix, 4% strand | Q71B31 |
| B, C, D, G, H, d, e, k | Gag protein | protein | 220 | 55% helix, 2% strand | Q71B31 |
| J | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 164 | 14% helix, 34% strand | P62937 |
| N, j | Gag protein | protein | 74 | 61% helix, 0% strand | Q71B31 |
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 | 795 | 0.74 | 0.79 | 89 | empty |
| 2 | 1195 | 0.74 | 0.77 | 107 | empty |
| 3 | 561 | 0.69 | 0.78 | 59 | empty |
| 4 | 549 | 0.67 | 0.77 | 37 | empty |
| 5 | 399 | 0.66 | 0.79 | 47 | empty |
Interfaces
24 interfaces between chains.
- C–D · 1149 Ų buried · 7 hydrogen bonds · protein-protein
- G–k · 1099 Ų buried · 8 hydrogen bonds · protein-protein
- e–k · 1089 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1054 Ų buried · 4 hydrogen bonds · protein-protein
- Y–e · 999 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6ZDJ · 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 Q71B31
- Every structure of UniProt P62937
- Elsewhere: RCSB PDB 6ZDJ · PDBe 6ZDJ · UniProt Q71B31 · UniProt P62937
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