Research workbench
Crystal structure of the Y186F mutant of KIJD10, a 3-ketoreductase from actinomadura kijaniata in complex with tdp-benzene and NADP
Analyse Crystal structure of the Y186F mutant of KIJD10, a 3-ketoreductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RC7
- Type
- protein
- Length
- 325 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar 3-ketoreductase
- UniProt
- B3TMR8
- Ligands
- NAP, TLO, NA, CL, PO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar 3-ketoreductase | protein | 325 | 39% helix, 30% strand | B3TMR8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- TLO · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phenoxy) phosphoryl]oxy}phosphoryl]thymidine · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.68 | 0.81 | 42 | NAP, TLO, CL |
| 2 | 135 | 0.52 | 0.80 | 31 | empty |
| 3 | 62 | 0.35 | 0.78 | 14 | empty |
| 4 | 66 | 0.34 | 0.76 | 14 | empty |
Compared structures
- 3RC7 · Crystal Structure of the Y186F mutant of KijD10, a 3-ketoreductase from Actinomadura… · the same entry in another collection · chain A against A, TM-score 1.00
- B3TMR8 · AlphaFold monomer V2.0 prediction for dtdp-3,4-didehydro-2,6-dideoxy- alpha-D-glucose… · 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 B3TMR8
- Elsewhere: RCSB PDB 3RC7 · PDBe 3RC7 · UniProt B3TMR8
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