Research workbench
Citrobacter freundii tyrosine phenol-lyase complexed with 4- hydroxypyridine and aminoacrylate from 3-F-L-tyrosine
Analyse Citrobacter freundii tyrosine phenol-lyase complexed with 4- hydroxypyridine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MPD
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine phenol-lyase
- EC
- 4.1.99.2
- UniProt
- P31013
- Ligands
- CQG, 0JO, YOF, K
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 455 | 44% helix, 15% strand | P31013 |
Ligands and binding sites
- CQG · pyridin-4-ol · ligand · 3 copies · chains A, B
- 0JO · 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid · ligand · chains A, B
- YOF · 3-fluorotyrosine · ligand · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.81 | 0.98 | 42 | CQG, 0JO |
| 2 | 677 | 0.74 | 0.80 | 56 | YOF |
| 3 | 500 | 0.73 | 0.82 | 48 | CQG |
| 4 | 524 | 0.71 | 0.80 | 45 | empty |
| 5 | 107 | 0.54 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2438 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, cofactor).
Compared structures
- 6MPD · Citrobacter freundii tyrosine phenol-lyase complexed with 4-hydroxypyridine and… · the same entry in another collection · chain A against A, TM-score 1.00
- P31013 · AlphaFold monomer V2.0 prediction for tyrosine phenol-lyase (P31013) · a predicted model of the same protein · 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 P31013
- Elsewhere: RCSB PDB 6MPD · PDBe 6MPD · UniProt P31013
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