MolNFT v1 · #82651 · protein
Crystal structure of hype-hypf complex
3VTI · Hydrogenase maturation factor: “Crystal structure of hype-hypf complex”. X-ray diffraction, 3 ligands (ZN, FE, MG), 19 pockets (best druggability 0.87). MolNFT v1 #82651 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VTI
- Type
- protein
- Length
- 2,098 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase maturation factor
- EC
- 2.1.3.-
- UniProt
- Q8RDB0, Q8RDA7
- Ligands
- ZN, FE, MG
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hydrogenase maturation factor (EC 2.1.3.-) | protein | 744 | 35% helix, 21% strand | Q8RDB0 |
| C, D | Hydrogenase maturation factor | protein | 305 | 35% helix, 27% strand | Q8RDA7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.87 | 0.88 | 117 | empty |
| 2 | 978 | 0.87 | 0.88 | 106 | empty |
| 3 | 1085 | 0.80 | 0.81 | 80 | MG |
| 4 | 1036 | 0.78 | 0.80 | 70 | MG |
| 5 | 932 | 0.73 | 0.77 | 88 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2445 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1169 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1117 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3VTI · Crystal structure of HypE-HypF complex · the same entry in another collection · chain B against B, 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
- Every structure of UniProt Q8RDA7
- Elsewhere: RCSB PDB 3VTI · PDBe 3VTI · UniProt Q8RDB0 · UniProt Q8RDA7
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