Research workbench
Crystal structure of fe-hydrogenase from methanothermobacter marburgensis in complex with 2-naphthylisocyanide
Analyse Crystal structure of fe-hydrogenase from methanothermobacter marburgensis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JJF
- Type
- protein
- Length
- 688 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
- UniProt
- P32440
- Ligands
- FE9, N2I
- Pockets
- 4 · best druggability 0.66
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 | 344 | 55% helix, 13% strand | P32440 |
Ligands and binding sites
- FE9 · iron-guanylyl pyridinol cofactor · ligand · 2 copies · chains A, B
- N2I · N-(naphthalen-2-yl)methanimine · ligand · 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 | 524 | 0.66 | 0.77 | 49 | FE9, N2I |
| 2 | 473 | 0.64 | 0.76 | 48 | FE9, N2I |
| 3 | 120 | 0.42 | 0.76 | 23 | empty |
| 4 | 100 | 0.37 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3830 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4JJF · Crystal structure of FE-hydrogenase from methanothermobacter marburgensis in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P32440 · AlphaFold monomer V2.0 prediction for 5,10-methenyltetrahydromethanopterin hydrogenase… · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P32440
- Elsewhere: RCSB PDB 4JJF · PDBe 4JJF · UniProt P32440
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.