Research workbench
Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from bacteroides thetaiotaomicron vpi-5482 at 2.00 a resolution (orthorhombic form with pyridoxal)
Analyse Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MBH
- Type
- protein
- Length
- 1,732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphomethylpyrimidine kinase
- UniProt
- Q89ZB9
- Ligands
- PXL, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Putative phosphomethylpyrimidine kinase | protein | 290 | 38% helix, 23% strand | Q89ZB9 |
| B | Putative phosphomethylpyrimidine kinase | protein | 287 | 39% helix, 23% strand | Q89ZB9 |
| C | Putative phosphomethylpyrimidine kinase | protein | 289 | 38% helix, 21% strand | Q89ZB9 |
| D | Putative phosphomethylpyrimidine kinase | protein | 286 | 38% helix, 23% strand | Q89ZB9 |
Ligands and binding sites
- PXL · 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C, E, F
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 | 1196 | 0.85 | 0.86 | 127 | empty |
| 2 | 624 | 0.83 | 0.87 | 82 | empty |
| 3 | 718 | 0.81 | 0.85 | 81 | empty |
| 4 | 138 | 0.78 | 0.96 | 36 | PXL |
| 5 | 128 | 0.78 | 0.96 | 36 | PXL |
Interfaces
11 interfaces between chains.
- B–E · 2013 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1897 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1866 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 765 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 731 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 modified (engineered).
Compared structures
- 3MBH · Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q89ZB9
- Elsewhere: RCSB PDB 3MBH · PDBe 3MBH · UniProt Q89ZB9
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