MolNFT v1 · #38972 · protein
Crystal structure of hypb from methanocaldococcus jannaschii in the triphosphate form, in complex with zinc
2HF8 · Probable hydrogenase nickel incorporation protein hypb: “Crystal structure of hypb from methanocaldococcus jannaschii in the triphosphate form, in complex with zinc”. X-ray diffraction, 3 ligands (GSP, ZN, MG), 3 pockets (best…
- PDB
- 2HF8
- 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, ZN, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable hydrogenase nickel incorporation protein hypb | protein | 211 | 45% helix, 19% strand | Q57884 |
| B | Probable hydrogenase nickel incorporation protein hypb | protein | 209 | 45% helix, 20% strand | Q57884 |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium 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 | 272 | 0.69 | 0.84 | 37 | GSP |
| 2 | 237 | 0.66 | 0.84 | 36 | GSP |
| 3 | 59 | 0.25 | 0.72 | 16 | ZN |
Interfaces
1 interface between chains.
- A–B · 1325 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2HF8 · Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form, in… · 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 2HF8 · PDBe 2HF8 · UniProt Q57884
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