MolNFT v1 · #77344 · protein
Crystal structure of KIJD10, a 3-ketoreductase from actinomadura kijaniata incomplex with NADP and tdp-benzene
3RC1 · Sugar 3-ketoreductase: “Crystal structure of KIJD10, a 3-ketoreductase from actinomadura kijaniata incomplex with NADP and tdp-benzene”. X-ray diffraction, 5 ligands (TLO, NAP, NA), 4 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 3RC1
- 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
- TLO, NAP, NA, CL, PO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar 3-ketoreductase | protein | 325 | 38% helix, 30% strand | B3TMR8 |
Ligands and binding sites
- TLO · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phenoxy) phosphoryl]oxy}phosphoryl]thymidine · ligand · chains A
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 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 | 340 | 0.69 | 0.82 | 41 | TLO, NAP, CL |
| 2 | 174 | 0.55 | 0.80 | 36 | empty |
| 3 | 61 | 0.36 | 0.78 | 13 | empty |
| 4 | 74 | 0.34 | 0.76 | 14 | empty |
Compared structures
- 3RC1 · Crystal Structure of KijD10, a 3-ketoreductase from Actinomadura kijaniata incomplex with… · 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 3RC1 · PDBe 3RC1 · UniProt B3TMR8
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