MolNFT v1 · #139657 · protein
Mycobacterium tuberculosis pantothenate kinase mutant F247A
5XMB: “Mycobacterium tuberculosis pantothenate kinase mutant F247A”. X-ray diffraction, 1 ligand (SO4), 18 pockets (best druggability 0.85). MolNFT v1 #139657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XMB
- Type
- protein
- Length
- 1,069 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- P9WPA7
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate kinase (EC 2.7.1.33) | protein | 278 | 41% helix, 21% strand | P9WPA7 |
| B | Pantothenate kinase (EC 2.7.1.33) | protein | 267 | 43% helix, 22% strand | P9WPA7 |
| C | Pantothenate kinase (EC 2.7.1.33) | protein | 260 | 44% helix, 23% strand | P9WPA7 |
| D | Pantothenate kinase (EC 2.7.1.33) | protein | 264 | 45% helix, 22% strand | P9WPA7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.85 | 0.86 | 121 | empty |
| 2 | 588 | 0.84 | 0.89 | 62 | empty |
| 3 | 551 | 0.72 | 0.80 | 45 | SO4 |
| 4 | 863 | 0.68 | 0.75 | 52 | empty |
| 5 | 468 | 0.68 | 0.79 | 37 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1930 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1155 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 391 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 P9WPA7
- Elsewhere: RCSB PDB 5XMB · PDBe 5XMB · UniProt P9WPA7
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