Research workbench
Immature HIV-1 matrix structure
Analyse Immature HIV-1 matrix structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OVQ
- Type
- protein
- Length
- 2,760 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag polyprotein
- UniProt
- B6DRA0
- Ligands
- MYR
- Pockets
- 20 · best druggability 0.64
Structure
electron microscopy · 1 distinct chain · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, P, b, E, Q, c, F, R, d, S, f, I, h, K, X, M, Y, Z, l, O, m | Gag polyprotein | protein | 115 | 67% helix, 3% strand | B6DRA0 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 24 copies · chains A, B, C, D, P, b, E, Q, c, F, R, d, S, f, I, h, K, X, M, Y, Z, l, O, m
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.64 | 0.73 | 116 | empty |
| 2 | 792 | 0.63 | 0.73 | 122 | empty |
| 3 | 431 | 0.55 | 0.74 | 69 | empty |
| 4 | 452 | 0.55 | 0.73 | 60 | empty |
| 5 | 419 | 0.54 | 0.74 | 63 | empty |
Interfaces
24 interfaces between chains.
- E–O · 77 Ų buried · 0 hydrogen bonds · protein-protein
- b–l · 76 Ų buried · 0 hydrogen bonds · protein-protein
- P–S · 75 Ų buried · 0 hydrogen bonds · protein-protein
- F–I · 72 Ų buried · 0 hydrogen bonds · protein-protein
- c–f · 72 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 lipid (myristoylation).
Compared structures
- 7OVQ · Immature HIV-1 matrix structure · 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 B6DRA0
- Elsewhere: RCSB PDB 7OVQ · PDBe 7OVQ · UniProt B6DRA0
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