MolNFT v1 · #92751 · protein
Crystal structure of klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue
4GI7: “Crystal structure of klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue”. X-ray diffraction, 3 ligands (ADP, 0JR, UNX), 20 pockets (best druggability 0.89). MolNFT v1 #92751 on GenesisL1: 3D structure…
- PDB
- 4GI7
- Type
- protein
- Length
- 2,459 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- B5XYG3
- Ligands
- ADP, 0JR, UNX
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, F | Pantothenate kinase (EC 2.7.1.33) | protein | 309 | 52% helix, 17% strand | B5XYG3 |
| D, G | Pantothenate kinase (EC 2.7.1.33) | protein | 308 | 52% helix, 19% strand | B5XYG3 |
| E | Pantothenate kinase (EC 2.7.1.33) | protein | 304 | 50% helix, 17% strand | B5XYG3 |
| H | Pantothenate kinase (EC 2.7.1.33) | protein | 303 | 51% helix, 18% strand | B5XYG3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, C, B, D, E, F, G, H
- 0JR · (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}butanamide · ligand · 5 copies · chains A, C, B, D, F
- UNX · Unknown atom or ion · ion · 45 copies · chains A, C, B, D, F, E, G, H
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 | 911 | 0.89 | 0.91 | 101 | empty |
| 2 | 740 | 0.87 | 0.91 | 76 | UNX |
| 3 | 805 | 0.87 | 0.90 | 71 | UNX |
| 4 | 711 | 0.87 | 0.91 | 70 | empty |
| 5 | 668 | 0.83 | 0.87 | 92 | ADP, 0JR, UNX |
Interfaces
16 interfaces between chains.
- A–C · 1978 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1956 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1943 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1922 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 548 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GI7 · Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a… · the same entry in another collection · chain B against B, TM-score 1.00
- B5XYG3 · AlphaFold monomer V2.0 prediction for pantothenate kinase (B5XYG3) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 B5XYG3
- Elsewhere: RCSB PDB 4GI7 · PDBe 4GI7 · UniProt B5XYG3
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