MolNFT v1 · #170831 · protein
Asymmetric [fe]-hydrogenase from methanolacinia paynteri apo and in complex with fegp at 2.1-a resolution
6YKA · 5,10-methenyltetrahydromethanopterin hydrogenase: “Asymmetric [fe]-hydrogenase from methanolacinia paynteri apo and in complex with fegp at 2.1-a resolution”. X-ray diffraction, 1 ligand (FE9), 4 pockets (best druggability 0.78).…
- PDB
- 6YKA
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5,10-methenyltetrahydromethanopterin hydrogenase
- EC
- 1.12.98.2
- Ligands
- FE9
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5,10-methenyltetrahydromethanopterin hydrogenase (EC 1.12.98.2) | protein | 341 | 55% helix, 13% strand | — |
Ligands and binding sites
- FE9 · iron-guanylyl pyridinol cofactor · ligand · chains B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.78 | 0.86 | 52 | EDO |
| 2 | 578 | 0.66 | 0.76 | 54 | EDO, FE9 |
| 3 | 90 | 0.42 | 0.78 | 26 | EDO |
| 4 | 52 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 4280 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 6YKA · Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at… · 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
- Elsewhere: RCSB PDB 6YKA · PDBe 6YKA
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