MolNFT v1 · #146855 · protein
Citrobacter freundii tyrosine phenol-lyase complexed with L- phenylalanine
6DUR: “Citrobacter freundii tyrosine phenol-lyase complexed with L- phenylalanine”. X-ray diffraction, 3 ligands (P71, P70, K), 11 pockets (best druggability 0.80). MolNFT v1 #146855 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6DUR
- Type
- protein
- Length
- 907 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
- P71, P70, K
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 452 | 46% helix, 14% strand | P31013 |
| B | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 455 | 45% helix, 15% strand | P31013 |
Ligands and binding sites
- P71 · (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4(1H)-ylidene}methyl]imino}-3-phenylpropanoic acid · ligand · chains A, B
- P70 · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)-L-phenylalanine · ligand · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.80 | 0.84 | 78 | P71 |
| 2 | 710 | 0.78 | 0.82 | 75 | P70 |
| 3 | 499 | 0.72 | 0.81 | 48 | empty |
| 4 | 523 | 0.72 | 0.81 | 46 | empty |
| 5 | 171 | 0.52 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2451 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6DUR · Citrobacter freundii tyrosine phenol-lyase complexed with L-phenylalanine · 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 0.96
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 6DUR · PDBe 6DUR · UniProt P31013
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