MolNFT v1 · #139043 · protein
Crystal structure of pseudomonas putida methionine gamma-lyase C116H mutant with L-methionine intermediates
5X2Z · L-methionine gamma-lyase: “Crystal structure of pseudomonas putida methionine gamma-lyase C116H mutant with L-methionine intermediates”. X-ray diffraction, 1 ligand (3LM), 12 pockets (best druggability 0.91). MolNFT v1 #139043 on…
- PDB
- 5X2Z
- 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
- Ligands
- 3LM
- Pockets
- 12 · best druggability 0.91
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% 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 | 44% helix, 16% strand | P13254 |
| D | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2) | protein | 396 | 44% helix, 15% 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.91 | 0.93 | 128 | 3LM |
| 2 | 647 | 0.87 | 0.91 | 82 | 3LM |
| 3 | 546 | 0.87 | 0.93 | 62 | 3LM |
| 4 | 767 | 0.84 | 0.87 | 131 | empty |
| 5 | 176 | 0.49 | 0.77 | 35 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2634 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2576 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1607 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1600 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 753 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5X2Z · Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant 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 0.97
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 5X2Z · PDBe 5X2Z · UniProt P13254
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