Research workbench
Crystal structure of P-cresol methylhydroxylase with substrate bound
Analyse Crystal structure of P-cresol methylhydroxylase with substrate bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DIQ
- Type
- protein
- Length
- 1,178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-cresol methylhydroxylase
- EC
- 1.17.99.1
- UniProt
- P09788, P09787
- Ligands
- FAD, PCR, HEC, CL
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | P-cresol methylhydroxylase (EC 1.17.99.1) | protein | 515 | 38% helix, 20% strand | P09788 |
| C, D | P-cresol methylhydroxylase (EC 1.17.99.1) | protein | 74 | 47% helix, 0% strand | P09787 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PCR · P-cresol · ligand · 2 copies · chains A, B
- HEC · Heme C · ligand · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.88 | 0.97 | 53 | FAD, PCR |
| 2 | 369 | 0.87 | 0.96 | 52 | FAD, PCR |
| 3 | 1086 | 0.86 | 0.87 | 95 | empty |
| 4 | 76 | 0.75 | 0.98 | 18 | empty |
| 5 | 250 | 0.73 | 0.87 | 30 | HEC |
Interfaces
3 interfaces between chains.
- A–B · 3711 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1029 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1027 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (heme c attachment, flavinylation).
Compared structures
- 1DIQ · Crystal structure of P-cresol methylhydroxylase with substrate bound · the same entry in another collection · chain D against D, TM-score 1.00
- P09788 · AlphaFold monomer V2.0 prediction for 4-cresol dehydrogenase [hydroxylating] flavoprotein… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P09787 · AlphaFold monomer V2.0 prediction for 4-cresol dehydrogenase [hydroxylating] cytochrome C… · a predicted model of the same protein · chain D 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 P09788
- Every structure of UniProt P09787
- Elsewhere: RCSB PDB 1DIQ · PDBe 1DIQ · UniProt P09788 · UniProt P09787
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