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
- 7BQW
- Type
- protein
- Length
- 1,415 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, 4.4.1.28
- UniProt
- Q8RDT4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% 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 | 367 | 40% helix, 17% strand | Q8RDT4 |
| B | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2, 4.4.1.28) | protein | 355 | 39% helix, 17% strand | Q8RDT4 |
| C | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2, 4.4.1.28) | protein | 343 | 38% helix, 17% strand | Q8RDT4 |
| D | L-methionine gamma-lyase (EC 4.4.1.11, 4.4.1.2, 4.4.1.28) | protein | 350 | 43% helix, 18% strand | Q8RDT4 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.76 | 0.83 | 65 | empty |
| 2 | 779 | 0.74 | 0.79 | 70 | empty |
| 3 | 716 | 0.72 | 0.78 | 73 | empty |
| 4 | 54 | 0.71 | 0.99 | 27 | empty |
| 5 | 554 | 0.67 | 0.77 | 64 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2063 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2004 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1604 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1580 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 744 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7BQW · Crystal structure of Methionine gamma-lyase from Fusobacterium nucleatum · the same entry in another collection · chain D against D, TM-score 1.00
- Q8RDT4 · AlphaFold monomer V2.0 prediction for L-methionine gamma-lyase (Q8RDT4) · a predicted model of the same protein · chain D 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 7BQW · PDBe 7BQW · UniProt Q8RDT4
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