Research workbench
Hybrid cluster protein (hcp) from methanothermobacter marburgensis
Analyse Hybrid cluster protein (hcp) from methanothermobacter marburgensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E0L
- Type
- protein
- Length
- 1,972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxylamine reductase
- EC
- 1.7.99.1
- UniProt
- D9PYV4
- Ligands
- FS2, SF4, FE
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, M | Hydroxylamine reductase (EC 1.7.99.1) | protein | 493 | 40% helix, 16% strand | D9PYV4 |
Ligands and binding sites
- FS2 · Fe-S-O hybrid cluster · ligand · 4 copies · chains A, B, K, M
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, K, M
- FE · Fe (III) ion · metal · 4 copies · chains A, B, K, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.81 | 0.98 | 24 | empty |
| 2 | 138 | 0.81 | 0.98 | 25 | empty |
| 3 | 1031 | 0.79 | 0.80 | 83 | empty |
| 4 | 70 | 0.68 | 0.94 | 29 | empty |
| 5 | 172 | 0.65 | 0.85 | 45 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3725 Ų buried · 58 hydrogen bonds · protein-protein
- K–M · 3626 Ų buried · 51 hydrogen bonds · protein-protein
- B–M · 325 Ų buried · 0 hydrogen bonds · protein-protein
- A–M · 123 Ų buried · 0 hydrogen bonds · protein-protein
- A–K · 99 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 7E0L · Class III hybrid cluster protein (HCP) from Methanothermobacter marburgensis · 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 D9PYV4
- Elsewhere: RCSB PDB 7E0L · PDBe 7E0L · UniProt D9PYV4
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