Research workbench
Crystal structure of short-chain DEHYDROGENASE/REDUCTASE of unknown function from caenorhabditis elegans with cofactor
Analyse Crystal structure of short-chain DEHYDROGENASE/REDUCTASE of unknown function… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XKQ
- Type
- protein
- Length
- 1,085 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain reductase family member (5D234)
- UniProt
- Q9N5G4
- Ligands
- NDP
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain reductase family member (5D234) | protein | 272 | 51% helix, 14% strand | Q9N5G4 |
| B, C, D | Short-chain reductase family member (5D234) | protein | 271 | 52% helix, 14% strand | Q9N5G4 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.84 | 0.85 | 78 | empty |
| 2 | 869 | 0.83 | 0.85 | 76 | NDP |
| 3 | 845 | 0.83 | 0.85 | 71 | NDP |
| 4 | 917 | 0.81 | 0.83 | 75 | NDP |
| 5 | 891 | 0.81 | 0.83 | 79 | NDP |
Interfaces
6 interfaces between chains.
- A–B · 1507 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1492 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1491 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1479 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 919 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1XKQ · Crystal Structure of Short-Chain Dehydrogenase/Reductase of unknown Function from… · the same entry in another collection · chain C against C, 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 Q9N5G4
- Elsewhere: RCSB PDB 1XKQ · PDBe 1XKQ · UniProt Q9N5G4
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