Research workbench
Crystal structure of T.KODAKARENSIS hypf
Analyse Crystal structure of T.KODAKARENSIS hypf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G9I
- Type
- protein
- Length
- 4,573 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase maturation protein hypf
- UniProt
- Q5JII4
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrogenase maturation protein hypf | protein | 766 | 33% helix, 13% strand | Q5JII4 |
| B, E, F | Hydrogenase maturation protein hypf | protein | 762 | 32% helix, 12% strand | Q5JII4 |
| C | Hydrogenase maturation protein hypf | protein | 756 | 34% helix, 13% strand | Q5JII4 |
| D | Hydrogenase maturation protein hypf | protein | 765 | 31% helix, 14% strand | Q5JII4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 18 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.87 | 0.88 | 128 | empty |
| 2 | 1150 | 0.87 | 0.88 | 130 | empty |
| 3 | 745 | 0.86 | 0.89 | 74 | empty |
| 4 | 996 | 0.85 | 0.86 | 99 | empty |
| 5 | 1041 | 0.84 | 0.85 | 103 | empty |
Interfaces
5 interfaces between chains.
- C–F · 1044 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 1042 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 619 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 495 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 107 modified (engineered).
Compared structures
- 4G9I · Crystal structure of T.kodakarensis HypF · 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 Q5JII4
- Elsewhere: RCSB PDB 4G9I · PDBe 4G9I · UniProt Q5JII4
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