MolNFT v1 · #163595 · protein
Crystal structure of ergothioneine degrading enzyme ergothionase from treponema denticola in complex with desmethyl-ergothioneine sulfonic acid
6S7Q: “Crystal structure of ergothioneine degrading enzyme ergothionase from treponema denticola in complex with…”. X-ray diffraction, 1 ligand (KZ5), 20 pockets (best druggability 0.79). MolNFT v1 #163595 on GenesisL1: 3D structure…
- PDB
- 6S7Q
- Type
- protein
- Length
- 3,976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ergothionase
- UniProt
- M2BPW8
- Ligands
- KZ5
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Ergothionase | protein | 497 | 59% helix, 6% strand | M2BPW8 |
Ligands and binding sites
- KZ5 · (2~{S})-2-(dimethylamino)-3-(2-sulfo-1~{H}-imidazol-4-yl)propanoic acid · ligand · 8 copies · chains A, B, D, C, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.79 | 0.97 | 37 | KZ5 |
| 2 | 141 | 0.79 | 0.96 | 44 | KZ5 |
| 3 | 102 | 0.78 | 0.97 | 31 | KZ5 |
| 4 | 89 | 0.77 | 0.99 | 28 | KZ5 |
| 5 | 87 | 0.73 | 0.96 | 26 | empty |
Interfaces
16 interfaces between chains.
- C–D · 3621 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3613 Ų buried · 59 hydrogen bonds · protein-protein
- E–H · 3545 Ų buried · 52 hydrogen bonds · protein-protein
- A–D · 3492 Ų buried · 54 hydrogen bonds · protein-protein
- F–G · 3475 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6S7Q · Crystal structure of ergothioneine degrading enzyme Ergothionase from Treponema denticola… · the same entry in another collection · chain A 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 M2BPW8
- Elsewhere: RCSB PDB 6S7Q · PDBe 6S7Q · UniProt M2BPW8
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