MolNFT v1 · #146888 · protein
Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-phenylalanine
6DVX: “Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-phenylalanine”. X-ray diffraction, 3 ligands (P71, P70, K), 7 pockets (best druggability 0.79). MolNFT v1 #146888 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6DVX
- Type
- protein
- Length
- 906 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
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 451 | 44% helix, 14% strand | P31013 |
| B | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 455 | 43% 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
- 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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.79 | 0.83 | 76 | P70 |
| 2 | 493 | 0.78 | 0.86 | 63 | P71 |
| 3 | 552 | 0.71 | 0.80 | 50 | empty |
| 4 | 532 | 0.71 | 0.80 | 50 | empty |
| 5 | 235 | 0.60 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2407 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6DVX · Citrobacter freundii tyrosine phenol-lyase F448A mutant 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 0.98
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 6DVX · PDBe 6DVX · UniProt P31013
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