Research workbench
[fe]-hydrogenase from methanolacinia paynteri in complex with gmp at 1.55-a resolution
Analyse [fe]-hydrogenase from methanolacinia paynteri in complex with gmp at 1.55-a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YKB
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5,10-methenyltetrahydromethanopterin [fe]-hydrogenase
- EC
- 1.12.98.2
- Ligands
- 5GP
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5,10-methenyltetrahydromethanopterin [fe]-hydrogenase (EC 1.12.98.2) | protein | 341 | 55% helix, 13% strand | — |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, C
- FMT · Formic acid · additive · 8 copies · chains A, C
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.78 | 0.86 | 53 | 5GP |
| 2 | 486 | 0.77 | 0.85 | 53 | 5GP, GOL |
Interfaces
1 interface between chains.
- A–C · 4613 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6YKB · [Fe]-hydrogenase from Methanolacinia paynteri in complex with GMP at 1.55-A resolution · 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 6YKB · PDBe 6YKB
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