MolNFT v1 · #139040 · protein
Crystal structure of pseudomonas putida methionine gamma-lyase wild type with L-methionine intermediates
5X2W · L-methionine gamma-lyase: “Crystal structure of pseudomonas putida methionine gamma-lyase wild type with L-methionine intermediates”. X-ray diffraction, 1 ligand (3LM), 10 pockets (best druggability 0.78). MolNFT v1 #139040 on…
- PDB
- 5X2W
- Type
- protein
- Length
- 1,574 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
- Ligands
- 3LM
- Pockets
- 10 · best druggability 0.78
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 | 42% helix, 15% strand | P13254 |
| D | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2) | protein | 398 | 41% helix, 16% strand | P13254 |
Ligands and binding sites
- 3LM · (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.78 | 0.87 | 74 | empty |
| 2 | 302 | 0.78 | 0.89 | 61 | empty |
| 3 | 614 | 0.77 | 0.83 | 78 | 3LM |
| 4 | 543 | 0.77 | 0.84 | 77 | 3LM |
| 5 | 548 | 0.76 | 0.83 | 70 | 3LM |
Interfaces
6 interfaces between chains.
- A–B · 2697 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2691 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1583 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1569 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 770 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5X2W · Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with… · 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 5X2W · PDBe 5X2W · UniProt P13254
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