Research workbench
Crystal structure of hypb from methanocaldococcus jannaschii in the triphosphate form
Analyse Crystal structure of hypb from methanocaldococcus jannaschii in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HF9
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable hydrogenase nickel incorporation protein hypb
- UniProt
- Q57884
- Ligands
- GSP, MG, ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable hydrogenase nickel incorporation protein hypb | protein | 211 | 44% helix, 19% strand | Q57884 |
| B | Probable hydrogenase nickel incorporation protein hypb | protein | 209 | 41% helix, 20% strand | Q57884 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.69 | 0.84 | 36 | MG, GSP |
| 2 | 257 | 0.68 | 0.84 | 37 | MG, GSP |
| 3 | 56 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1302 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2HF9 · Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form · the same entry in another collection · chain A against A, TM-score 1.00
- Q57884 · AlphaFold monomer V2.0 prediction for probable hydrogenase maturation factor hypb (Q57884) · a predicted model of the same protein · chain B 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 Q57884
- Elsewhere: RCSB PDB 2HF9 · PDBe 2HF9 · UniProt Q57884
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.