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Crystal structure of L-methionine gamma-lyase from pseudomonas putida C116H mutant complexed with L-homocysteine
Analyse Crystal structure of L-methionine gamma-lyase from pseudomonas putida C116H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VK4
- Type
- protein
- Length
- 1,572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine gamma-lyase
- EC
- 4.4.1.11
- UniProt
- P13254
- Ligands
- HCS
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Methionine gamma-lyase (EC 4.4.1.11) | protein | 392 | 42% helix, 17% strand | P13254 |
| B | Methionine gamma-lyase (EC 4.4.1.11) | protein | 396 | 41% helix, 16% strand | P13254 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.86 | 0.93 | 96 | empty |
| 2 | 377 | 0.73 | 0.84 | 39 | HCS |
| 3 | 521 | 0.72 | 0.81 | 54 | HCS |
| 4 | 413 | 0.71 | 0.82 | 38 | HCS |
| 5 | 526 | 0.71 | 0.80 | 53 | HCS |
Interfaces
6 interfaces between chains.
- A–B · 2732 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2729 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 1615 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1558 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 771 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 3VK4 · Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant… · the same entry in another collection · chain D against D, TM-score 1.00
- P13254 · AlphaFold monomer V2.0 prediction for L-methionine gamma-lyase (P13254) · a predicted model of the same protein · chain C 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 3VK4 · PDBe 3VK4 · UniProt P13254
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