Research workbench
[fe]-hydrogenase from methanolacinia paynteri with bound guanylylpyridinol at 1.7-a resolution
Analyse [fe]-hydrogenase from methanolacinia paynteri with bound guanylylpyridinol at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YK9
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5,10-methenyltetrahydromethanopterin hydrogenase
- EC
- 1.12.98.2
- Ligands
- GLY, 5GP, FEG, GMP
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | 5,10-methenyltetrahydromethanopterin hydrogenase (EC 1.12.98.2) | protein | 341 | 56% helix, 13% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, B
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains B, C
- FEG · 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine · ligand · chains A, E
- GMP · Guanosine · ligand · chains E
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.78 | 0.87 | 44 | FEG |
| 2 | 466 | 0.78 | 0.86 | 50 | GMP |
| 3 | 426 | 0.78 | 0.86 | 44 | 5GP |
| 4 | 454 | 0.76 | 0.84 | 52 | 5GP |
| 5 | 874 | 0.71 | 0.76 | 71 | empty |
Interfaces
5 interfaces between chains.
- B–C · 4571 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 4567 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 235 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 77 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 72 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YK9 · [Fe]-hydrogenase from Methanolacinia paynteri with bound guanylylpyridinol at 1.7-A… · 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 6YK9 · PDBe 6YK9
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