Research workbench
Structural genomics, unknown function crystal structure of E. COLI K-12 yqhd
Analyse Structural genomics, unknown function crystal structure of E. COLI K-12 yqhd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OJ7
- Type
- protein
- Length
- 1,560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical oxidoreductase yqhd
- UniProt
- Q46856
- Ligands
- NZQ, ZN, BO3, CL
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hypothetical oxidoreductase yqhd | protein | 390 | 52% helix, 14% strand | Q46856 |
Ligands and binding sites
- NZQ · 5,6-dihydroxy-nadp · ligand · 3 copies · chains A, B, D
- ZN · Zinc ion · metal · 3 copies · chains B, C, D
- BO3 · Boric acid · ion · 2 copies · chains A, C
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.81 | 0.82 | 114 | NZQ |
| 2 | 516 | 0.78 | 0.85 | 66 | NZQ |
| 3 | 98 | 0.76 | 0.97 | 25 | empty |
| 4 | 97 | 0.76 | 0.97 | 25 | empty |
| 5 | 732 | 0.75 | 0.81 | 82 | NZQ |
Interfaces
4 interfaces between chains.
- A–D · 1871 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1858 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 856 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1OJ7 · Structural genomics, unknown function crystal structure of E. COLI K-12 yqhd · the same entry in another collection · chain A against A, TM-score 1.00
- Q46856 · AlphaFold monomer V2.0 prediction for alcohol dehydrogenase yqhd (Q46856) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q46856
- Elsewhere: RCSB PDB 1OJ7 · PDBe 1OJ7 · UniProt Q46856
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