Research workbench
Crystal structure of type III pantothenate kinase (pank III) from burkholderia cenocepacia complexed with pantothenate, imidodiphosphate, and AMP
Analyse Crystal structure of type III pantothenate kinase (pank III) from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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