MolNFT v1 · #51912 · protein
Quinonoid intermediate of citrobacter freundii tyrosine phenol-lyase formed with alanine
2VLF: “Quinonoid intermediate of citrobacter freundii tyrosine phenol-lyase formed with alanine”. X-ray diffraction, 2 ligands (PLI, K), 11 pockets (best druggability 0.82). MolNFT v1 #51912 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VLF
- Type
- protein
- Length
- 911 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
- PLI, K
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 456 | 45% helix, 15% strand | P31013 |
| B | Tyrosine phenol-lyase (EC 4.1.99.2) | protein | 455 | 46% helix, 15% strand | P31013 |
Ligands and binding sites
- PLI · (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}propanoic acid · ligand · 2 copies · 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 B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.82 | 0.98 | 41 | PLI |
| 2 | 788 | 0.77 | 0.81 | 84 | PLI |
| 3 | 519 | 0.72 | 0.81 | 45 | empty |
| 4 | 498 | 0.71 | 0.81 | 45 | empty |
| 5 | 91 | 0.56 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2432 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2VLF · Quinonoid intermediate of Citrobacter freundii tyrosine phenol-lyase formed with alanine · the same entry in another collection · chain B against B, 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 2VLF · PDBe 2VLF · UniProt P31013
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