MolNFT v1 · #114300 · protein
Crystal structure of type III pantothenate kinase (pank III) from burkholderia cenocepacia complexed with pantothenate, imidodiphosphate, and AMP
5B8H: “Crystal structure of type III pantothenate kinase (pank III) from burkholderia cenocepacia complexed with…”. X-ray diffraction, 3 ligands (2PN, PAU, AMP), 3 pockets (best druggability 0.72). MolNFT v1 #114300 on GenesisL1: 3D…
- PDB
- 5B8H
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- B4E9P3
- Ligands
- 2PN, PAU, AMP
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III pantothenate kinase (EC 2.7.1.33) | protein | 256 | 39% helix, 27% strand | B4E9P3 |
| B | Type III pantothenate kinase (EC 2.7.1.33) | protein | 253 | 38% helix, 26% strand | B4E9P3 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 2 copies · chains A, B
- PAU · Pantothenoic acid · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.72 | 0.82 | 61 | 2PN, PAU |
| 2 | 382 | 0.71 | 0.82 | 53 | 2PN, PAU |
| 3 | 52 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2177 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 5B8H · Crystal Structure of Type III pantothenate kinase (PanK III) from Burkholderia… · the same entry in another collection · chain A against A, TM-score 1.00
- B4E9P3 · AlphaFold monomer V2.0 prediction for type III pantothenate kinase (B4E9P3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 B4E9P3
- Elsewhere: RCSB PDB 5B8H · PDBe 5B8H · UniProt B4E9P3
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