MolNFT v1 · #63441 · protein
Crystal structure of L-tyrosine decarboxylase mfna (ec 4.1.1.25) (NP_247014.1) from methanococcus jannaschii at 2.11 a resolution
3F9T: “Crystal structure of L-tyrosine decarboxylase mfna (ec 4.1.1.25) (NP_247014.1) from methanococcus jannaschii…”. X-ray diffraction, 1 ligand (PLP), 13 pockets (best druggability 0.79). MolNFT v1 #63441 on GenesisL1: 3D structure…
- PDB
- 3F9T
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-tyrosine decarboxylase mfna
- EC
- 4.1.1.25
- UniProt
- Q60358
- Ligands
- PLP
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-tyrosine decarboxylase mfna (EC 4.1.1.25) | protein | 394 | 44% helix, 14% strand | Q60358 |
| B | L-tyrosine decarboxylase mfna (EC 4.1.1.25) | protein | 392 | 45% helix, 15% strand | Q60358 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.79 | 0.98 | 34 | PLP |
| 2 | 131 | 0.78 | 0.96 | 36 | PLP |
| 3 | 105 | 0.44 | 0.79 | 28 | empty |
| 4 | 58 | 0.43 | 0.82 | 19 | empty |
| 5 | 59 | 0.40 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 5261 Ų buried · 88 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 3F9T · Crystal structure of L-tyrosine decarboxylase MfnA (EC 4.1.1.25) (NP_247014.1) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q60358 · AlphaFold monomer V2.0 prediction for L-TYROSINE/L-aspartate decarboxylase (Q60358) · 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 Q60358
- Elsewhere: RCSB PDB 3F9T · PDBe 3F9T · UniProt Q60358
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