Research workbench
Crystal structure of a type III pantothenate kinase: insight into the catalysis of an essential coenzyme a biosynthetic enzyme universally distributed in bacteria
Analyse Crystal structure of a type III pantothenate kinase: insight into the catalysis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GTD
- Type
- protein
- Length
- 1,488 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III pantothenate kinase
- EC
- 2.7.1.-
- UniProt
- Q9WZY5
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Type III pantothenate kinase (EC 2.7.1.-) | protein | 248 | 42% helix, 25% strand | Q9WZY5 |
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.83 | 0.88 | 87 | empty |
| 2 | 507 | 0.83 | 0.89 | 70 | empty |
| 3 | 478 | 0.83 | 0.90 | 69 | empty |
| 4 | 456 | 0.82 | 0.90 | 74 | empty |
| 5 | 583 | 0.82 | 0.88 | 71 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2186 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2143 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2069 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 626 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 606 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2GTD · Crystal Structure of a Type III Pantothenate Kinase: Insight into the Catalysis of an… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9WZY5 · AlphaFold monomer V2.0 prediction for type III pantothenate kinase (Q9WZY5) · a predicted model of the same protein · chain F 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 Q9WZY5
- Elsewhere: RCSB PDB 2GTD · PDBe 2GTD · UniProt Q9WZY5
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