Research workbench
Crystal structure of a quinonprotein alcohol dehydrogenase-like protein (BT1487) from bacteroides thetaiotaomicron vpi-5482 at 2.64 a resolution
Analyse Crystal structure of a quinonprotein alcohol dehydrogenase-like protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R5O
- Type
- protein
- Length
- 1,683 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quinonprotein alcohol dehydrogenase-like protein
- UniProt
- Q8A7N7
- Ligands
- CA, CL
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quinonprotein alcohol dehydrogenase-like protein | protein | 426 | 4% helix, 46% strand | Q8A7N7 |
| B, C | Quinonprotein alcohol dehydrogenase-like protein | protein | 416 | 4% helix, 47% strand | Q8A7N7 |
| D | Quinonprotein alcohol dehydrogenase-like protein | protein | 425 | 4% helix, 46% strand | Q8A7N7 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, C, B
- CL · Chloride ion · ion · 2 copies · chains A, C
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · 12 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.77 | 0.80 | 81 | 7PE, ACT |
| 2 | 972 | 0.77 | 0.79 | 78 | ACT |
| 3 | 915 | 0.76 | 0.79 | 86 | empty |
| 4 | 925 | 0.76 | 0.79 | 82 | empty |
| 5 | 416 | 0.68 | 0.80 | 51 | 7PE |
Interfaces
3 interfaces between chains.
- A–C · 659 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 506 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 247 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4R5O · Crystal structure of a Quinonprotein alcohol dehydrogenase-like protein (BT1487) from… · 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 Q8A7N7
- Elsewhere: RCSB PDB 4R5O · PDBe 4R5O · UniProt Q8A7N7
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