MolNFT v1 · #82346 · protein
Crystal structure of L-methionine gamma-lyase from pseudomonas putida C116H mutant.
3VK2: “Crystal structure of L-methionine gamma-lyase from pseudomonas putida C116H mutant.”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.86). MolNFT v1 #82346 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3VK2
- Type
- protein
- Length
- 1,574 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
- 12 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Methionine gamma-lyase (EC 4.4.1.11) | protein | 393 | 42% helix, 17% strand | P13254 |
| B | Methionine gamma-lyase (EC 4.4.1.11) | protein | 396 | 40% helix, 16% strand | P13254 |
| C | Methionine gamma-lyase (EC 4.4.1.11) | protein | 392 | 43% helix, 17% strand | P13254 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.86 | 0.90 | 91 | empty |
| 2 | 562 | 0.75 | 0.82 | 56 | SO4 |
| 3 | 460 | 0.74 | 0.83 | 36 | SO4 |
| 4 | 647 | 0.72 | 0.79 | 69 | SO4 |
| 5 | 460 | 0.71 | 0.81 | 39 | SO4 |
Interfaces
6 interfaces between chains.
- C–D · 2733 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2709 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 1559 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1550 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 774 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 3VK2 · Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant. · 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 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 3VK2 · PDBe 3VK2 · UniProt P13254
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