MolNFT v1 · #12025 · protein
Crystal structure of the streptococcus pneumoniae phosphomevalonate kinase (pmk)
1K47: “Crystal structure of the streptococcus pneumoniae phosphomevalonate kinase (pmk)”. X-ray diffraction, 19 pockets (best druggability 0.74). MolNFT v1 #12025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K47
- Type
- protein
- Length
- 1,932 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomevalonate kinase
- EC
- 2.7.4.2
- UniProt
- Q8DR49
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Phosphomevalonate kinase (EC 2.7.4.2) | protein | 322 | 45% helix, 23% strand | Q8DR49 |
Pockets
19 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.74 | 0.77 | 92 | empty |
| 2 | 906 | 0.73 | 0.77 | 89 | empty |
| 3 | 100 | 0.72 | 0.94 | 22 | empty |
| 4 | 106 | 0.71 | 0.93 | 22 | empty |
| 5 | 140 | 0.71 | 0.90 | 31 | empty |
Interfaces
12 interfaces between chains.
- B–F · 1281 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1269 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1261 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 769 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 755 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 1K47 · Crystal Structure of the Streptococcus pneumoniae Phosphomevalonate Kinase (PMK) · 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 Q8DR49
- Elsewhere: RCSB PDB 1K47 · PDBe 1K47 · UniProt Q8DR49
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