MolNFT v1 · #139041 · protein
Crystal structure of pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates
5X2X · L-methionine gamma-lyase: “Crystal structure of pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates”. X-ray diffraction, 2 ligands (4LM, H2S), 10 pockets (best druggability 0.86). MolNFT v1 #139041…
- PDB
- 5X2X
- 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
- 4LM, H2S
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% 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 | 398 | 43% helix, 16% strand | P13254 |
Ligands and binding sites
- 4LM · (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid · ligand · 4 copies · chains A, B, C, D
- H2S · Hydrosulfuric acid · ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.86 | 0.92 | 85 | empty |
| 2 | 272 | 0.70 | 0.85 | 52 | 4LM, H2S |
| 3 | 335 | 0.69 | 0.82 | 64 | 4LM, H2S |
| 4 | 315 | 0.68 | 0.82 | 67 | 4LM, H2S |
| 5 | 293 | 0.67 | 0.83 | 65 | 4LM, H2S |
Interfaces
6 interfaces between chains.
- C–D · 2696 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2681 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 1605 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1579 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 756 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5X2X · Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with… · the same entry in another collection · chain C against C, 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 0.98
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 5X2X · PDBe 5X2X · UniProt P13254
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