Research workbench
Crystal structure of full-length hypf in the phosphate- and nucleotide-bound form
Analyse Crystal structure of full-length hypf in the phosphate- and nucleotide-bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VTH
- Type
- protein
- Length
- 1,383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase maturation factor
- EC
- 2.1.3.-
- UniProt
- Q8RDB0
- Ligands
- APC, AP2, ZN, MG, FE, PO4
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrogenase maturation factor (EC 2.1.3.-) | protein | 753 | 36% helix, 21% strand | Q8RDB0 |
| B | Hydrogenase maturation factor (EC 2.1.3.-) | protein | 630 | 35% helix, 18% strand | Q8RDB0 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- AP2 · Phosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.87 | 0.89 | 84 | APC, MG, AP2 |
| 2 | 927 | 0.86 | 0.88 | 92 | APC, MG, AP2 |
| 3 | 475 | 0.79 | 0.87 | 59 | PO4, GOL |
| 4 | 481 | 0.77 | 0.85 | 50 | GOL |
| 5 | 114 | 0.58 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1184 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3VTH · Crystal structure of full-length HypF in the phosphate- and nucleotide-bound form · 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 Q8RDB0
- Elsewhere: RCSB PDB 3VTH · PDBe 3VTH · UniProt Q8RDB0
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