Research workbench
Detailed structure of L-methionine-lyase from pseudomonas putida
Analyse Detailed structure of L-methionine-lyase from pseudomonas putida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UKJ
- Type
- protein
- Length
- 1,592 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
- SO4
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Methionine gamma-lyase (EC 4.4.1.11) | protein | 398 | 40% helix, 17% strand | P13254 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.85 | 0.89 | 98 | SO4 |
| 2 | 511 | 0.75 | 0.83 | 39 | SO4 |
| 3 | 473 | 0.74 | 0.83 | 41 | SO4 |
| 4 | 523 | 0.73 | 0.81 | 36 | SO4 |
| 5 | 567 | 0.73 | 0.80 | 45 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 2597 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2587 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 1794 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1753 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 733 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 1UKJ · Detailed structure of L-Methionine-Lyase from Pseudomonas putida · 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 A against A, TM-score 0.99
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 1UKJ · PDBe 1UKJ · UniProt P13254
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