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Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin
Analyse Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LQW
- Type
- protein
- Length
- 625 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 sumo-protein ligase RANBP2; Capsid protein P24
- EC
- 6.3.2.-, 5.2.1.8
- UniProt
- P49792, P12497
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 sumo-protein ligase RANBP2 (EC 6.3.2.-, 5.2.1.8) | protein | 169 | 14% helix, 31% strand | P49792 |
| C | Capsid protein P24 | protein | 146 | 58% helix, 4% strand | P12497 |
| D | Capsid protein P24 | protein | 141 | 58% helix, 3% strand | P12497 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.72 | 0.95 | 18 | empty |
| 2 | 897 | 0.71 | 0.76 | 95 | empty |
| 3 | 339 | 0.59 | 0.77 | 39 | empty |
| 4 | 74 | 0.38 | 0.78 | 14 | empty |
| 5 | 99 | 0.33 | 0.72 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–D · 545 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 352 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4LQW · Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin · 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 P49792
- Every structure of UniProt P12497
- Elsewhere: RCSB PDB 4LQW · PDBe 4LQW · UniProt P49792 · UniProt P12497
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