Research workbench
Crystal structure of hypb from methanocaldococcus jannaschii in the triphosphate form, in complex with zinc
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
- 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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