Research workbench
Perdeuterated tyrosine phenol-lyase from citrobacter freundii complexed with an aminoacrylate intermediate formed from S-ethyl-L- cysteine and 4-hydroxypyridine
Analyse Perdeuterated tyrosine phenol-lyase from citrobacter freundii complexed with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NV8
- 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, DHA, K
- Pockets
- 12 · best druggability 0.80
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
- DHA · 2-amino-acrylic acid · 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
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 | 147 | 0.80 | 0.97 | 38 | CQG, 0JO |
| 2 | 708 | 0.75 | 0.80 | 54 | DHA |
| 3 | 520 | 0.71 | 0.80 | 47 | CQG |
| 4 | 512 | 0.70 | 0.80 | 48 | empty |
| 5 | 144 | 0.55 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2454 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, cofactor).
Compared structures
- 6NV8 · Perdeuterated tyrosine phenol-lyase from Citrobacter freundii complexed with an… · 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 6NV8 · PDBe 6NV8 · UniProt P31013
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