Research workbench
Crystal structure of dtdp-6-deoxy-L-lyxo-4-hexulose reductase (rmld) in complex with NADPH and dtdp-L-rhamnose
Analyse Crystal structure of dtdp-6-deoxy-L-lyxo-4-hexulose reductase (rmld) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KC3
- Type
- protein
- Length
- 298 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-glucose oxidoreductase
- EC
- 1.1.1.133
- UniProt
- P26392
- Ligands
- NDP, TRH, MG
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dtdp-glucose oxidoreductase (EC 1.1.1.133) | protein | 298 | 45% helix, 18% strand | P26392 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- TRH · 2'-deoxy-thymidine-beta-L-rhamnose · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.70 | 0.78 | 55 | NDP, TRH |
| 2 | 57 | 0.34 | 0.78 | 15 | empty |
Compared structures
- 1KC3 · Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P26392 · AlphaFold monomer V2.0 prediction for dtdp-4-dehydrorhamnose reductase (P26392) · 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 P26392
- Elsewhere: RCSB PDB 1KC3 · PDBe 1KC3 · UniProt P26392
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