Research workbench
Crystal structure of methionine gamma-lyase from fusobacterium nucleatum
Analyse Crystal structure of methionine gamma-lyase from fusobacterium nucleatum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LXU
- Type
- protein
- Length
- 391 residues
- Chains
- 1
- 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, 4.4.1.28
- UniProt
- Q8RDT4
- Ligands
- NO3
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2, 4.4.1.28) | protein | 391 | 41% helix, 16% strand | Q8RDT4 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.53 | 0.77 | 28 | NO3 |
| 2 | 150 | 0.44 | 0.75 | 25 | NO3 |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 6LXU · Crystal structure of methionine gamma-lyase from Fusobacterium nucleatum · the same entry in another collection · chain A against A, TM-score 1.00
- Q8RDT4 · AlphaFold monomer V2.0 prediction for L-methionine gamma-lyase (Q8RDT4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8RDT4
- Elsewhere: RCSB PDB 6LXU · PDBe 6LXU · UniProt Q8RDT4
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