MolNFT v1 · #139039 · protein
Crystal structure of pseudomonas putida methionine gamma-lyase wild type without sulfate ion
5X2V · L-methionine gamma-lyase: “Crystal structure of pseudomonas putida methionine gamma-lyase wild type without sulfate ion”. X-ray diffraction, 8 pockets (best druggability 0.86). MolNFT v1 #139039 on GenesisL1: 3D structure, binding…
- PDB
- 5X2V
- Type
- protein
- Length
- 1,572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-methionine gamma-lyase
- EC
- 4.4.1.11, 4.4.1.2
- UniProt
- P13254
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2) | protein | 392 | 43% helix, 16% strand | P13254 |
| D | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2) | protein | 396 | 42% helix, 16% strand | P13254 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.86 | 0.88 | 142 | empty |
| 2 | 565 | 0.74 | 0.81 | 69 | empty |
| 3 | 394 | 0.73 | 0.83 | 36 | empty |
| 4 | 494 | 0.72 | 0.81 | 48 | empty |
| 5 | 591 | 0.72 | 0.80 | 50 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2674 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2673 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1578 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1553 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 737 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5X2V · Crystal structure of Pseudomonas putida methionine gamma-lyase wild type without sulfate… · 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 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 5X2V · PDBe 5X2V · UniProt P13254
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