Research workbench
Type III pantothenate kinase from thermotoga maritima complexed with product phosphopantothenate
Analyse Type III pantothenate kinase from thermotoga maritima complexed with product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BF3
- Type
- protein
- Length
- 1,482 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III pantothenate kinase
- EC
- 2.7.1.33
- UniProt
- Q9WZY5
- Ligands
- PAZ, MG
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Type III pantothenate kinase (EC 2.7.1.33) | protein | 248 | 42% helix, 25% strand | Q9WZY5 |
| C, D | Type III pantothenate kinase (EC 2.7.1.33) | protein | 245 | 41% helix, 24% strand | Q9WZY5 |
Ligands and binding sites
- PAZ · N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanine · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, D, F, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.83 | 0.86 | 107 | MG, PAZ |
| 2 | 621 | 0.83 | 0.88 | 87 | PAZ |
| 3 | 576 | 0.82 | 0.88 | 65 | PAZ |
| 4 | 628 | 0.82 | 0.87 | 82 | PAZ |
| 5 | 613 | 0.82 | 0.87 | 75 | PAZ |
Interfaces
12 interfaces between chains.
- E–F · 2108 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2092 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2084 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 580 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 575 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3BF3 · Type III pantothenate kinase from Thermotoga maritima complexed with product… · 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 C against A, TM-score 0.99
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 3BF3 · PDBe 3BF3 · UniProt Q9WZY5
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