MolNFT v1 · #159009 · protein
Structure of HIV-1 ca 1/2-hexamer
6OBH: “Structure of HIV-1 ca 1/2-hexamer”. X-ray diffraction, 1 ligand (NA), 15 pockets (best druggability 0.69). MolNFT v1 #159009 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OBH
- Type
- protein
- Length
- 1,302 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ca
- UniProt
- T2CI25, B6DRA0
- Ligands
- NA
- Pockets
- 15 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 61% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ca | protein | 220 | 60% helix, 2% strand | T2CI25 |
| B | Ca | protein | 214 | 62% helix, 0% strand | B6DRA0 |
| C | Ca | protein | 220 | 60% helix, 2% strand | T2CI25 |
| D | Ca | protein | 214 | 62% helix, 0% strand | T2CI25 |
| E | Ca | protein | 220 | 60% helix, 2% strand | B6DRA0 |
| F | Ca | protein | 214 | 62% helix, 0% strand | T2CI25 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.69 | 0.77 | 58 | empty |
| 2 | 663 | 0.68 | 0.77 | 60 | empty |
| 3 | 648 | 0.68 | 0.77 | 60 | empty |
| 4 | 672 | 0.67 | 0.76 | 62 | empty |
| 5 | 666 | 0.66 | 0.75 | 55 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1356 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1354 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1336 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1334 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1309 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6OBH · Structure of HIV-1 CA 1/2-hexamer · 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 T2CI25
- Every structure of UniProt B6DRA0
- Elsewhere: RCSB PDB 6OBH · PDBe 6OBH · UniProt T2CI25 · UniProt B6DRA0
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