MolNFT v1 · #188092 · protein
X-ray structure of the HIV-1 myristoylated matrix protein
7TBP · Capsid protein P24: “X-ray structure of the HIV-1 myristoylated matrix protein”. X-ray diffraction, 1 ligand (MYR), 2 pockets (best druggability 0.60). MolNFT v1 #188092 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TBP
- Type
- protein
- Length
- 309 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P24
- UniProt
- C1JB69
- Ligands
- MYR
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Capsid protein P24 | protein | 108 | 66% helix, 3% strand | C1JB69 |
| A | Capsid protein P24 | protein | 103 | 66% helix, 3% strand | C1JB69 |
| C | Capsid protein P24 | protein | 98 | 65% helix, 3% strand | C1JB69 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, A
- CIT · Citric acid · additive · 2 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.60 | 0.75 | 58 | empty |
| 2 | 232 | 0.50 | 0.75 | 34 | 1PE |
Interfaces
2 interfaces between chains.
- B–A · 224 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 155 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 7TBP · X-ray structure of the HIV-1 myristoylated matrix protein · the same entry in another collection · chain B against B, 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 C1JB69
- Elsewhere: RCSB PDB 7TBP · PDBe 7TBP · UniProt C1JB69
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