MolNFT v2 · #180234 · protein
Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates
7F1V · L-methionine gamma-lyase: “Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-homocysteine intermediates”. X-ray diffraction at 2.25, 2 ligands (7XF, HCS), 11 pockets (best druggability 0.82). MolNFT…
- PDB
- 7F1V
- Type
- protein
- Length
- 1,572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Pseudomonas putida
- Molecule
- L-methionine gamma-lyase
- EC
- 4.4.1.11, 4.4.1.2
- UniProt
- P13254
- Ligands
- 7XF, HCS
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.25 · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2) | protein | 396 | 42% helix, 16% strand | P13254 |
| B, C, D | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2) | protein | 392 | 42% helix, 16% strand | P13254 |
Ligands and binding sites
- 7XF · (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-sulfanyl-butanoic acid · ligand · 2 copies · chains A, B, C, D
- HCS · 2-amino-4-mercapto-butyric acid · ligand · chains C, D
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 | 222 | 0.82 | 0.95 | 43 | empty |
| 2 | 282 | 0.79 | 0.90 | 53 | empty |
| 3 | 519 | 0.75 | 0.82 | 59 | empty |
| 4 | 283 | 0.71 | 0.85 | 48 | 7XF |
| 5 | 335 | 0.69 | 0.83 | 56 | HCS |
Interfaces
6 interfaces between chains.
- A–B · 2682 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2669 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1591 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1559 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 752 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (cofactor, covalent ligand).
Compared structures
- 7F1V · Crystal structure of pseudomonas putida methionine gamma-lyase Q349S mutant with… · the same entry in another collection · chain A against A, TM-score 1.00
- P13254 · AlphaFold monomer V2.0 prediction for L-methionine gamma-lyase (P13254) · a predicted model of the same protein · chain B 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 P13254
- Elsewhere: RCSB PDB 7F1V · PDBe 7F1V · UniProt P13254
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