Research workbench
Mature HIV-1 matrix structure
Analyse Mature 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
- 7OVR
- Type
- protein
- Length
- 2,760 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 matrix
- UniProt
- B6DRA0
- Ligands
- MYR, PIO
- Pockets
- 20 · best druggability 0.53
Structure
electron microscopy · 1 distinct chain · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, I, J, O, P, Q, R, S, U, W, Y, b, c, d, e, f, j, l | HIV-1 matrix | protein | 115 | 67% helix, 3% strand | B6DRA0 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 24 copies · chains A, B, C, D, E, F, H, I, J, O, P, Q, R, S, U, W, Y, b, c, d, e, f, j, l
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 24 copies · chains A, D, B, Q, C, d, E, F, I, H, J, O, P, S, R, U, W, Y, b, c, f, e, j, l
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.53 | 0.73 | 60 | empty |
| 2 | 405 | 0.53 | 0.73 | 59 | empty |
| 3 | 404 | 0.53 | 0.73 | 61 | empty |
| 4 | 382 | 0.53 | 0.73 | 56 | empty |
| 5 | 403 | 0.53 | 0.73 | 60 | empty |
Interfaces
20 interfaces between chains.
- F–d · 65 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 65 Ų buried · 1 hydrogen bond · protein-protein
- E–c · 65 Ų buried · 1 hydrogen bond · protein-protein
- D–P · 65 Ų buried · 1 hydrogen bond · protein-protein
- E–Q · 64 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 lipid (myristoylation).
Compared structures
- 7OVR · Mature 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 7OVR · PDBe 7OVR · UniProt B6DRA0
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