MolNFT v1 · #135215 · protein
Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from rhizobium etli cfn 42 in complex with NADPH and oxalate
5TSD · Probable hydroxyacid dehydrogenase protein: “Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from rhizobium etli cfn 42 in complex with…”. X-ray diffraction, 2 ligands (NDP, OXD), 4 pockets (best druggability 0.79).…
- PDB
- 5TSD
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable hydroxyacid dehydrogenase protein
- UniProt
- Q2KDT2
- Ligands
- NDP, OXD
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable hydroxyacid dehydrogenase protein | protein | 316 | 34% helix, 16% strand | Q2KDT2 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- OXD · Oxalic acid · ligand · 2 copies · chains A, B
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 | 712 | 0.79 | 0.83 | 85 | NDP, OXD |
| 2 | 645 | 0.77 | 0.83 | 72 | NDP, OXD |
| 3 | 117 | 0.43 | 0.77 | 23 | empty |
| 4 | 96 | 0.39 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2465 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 5TSD · Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN… · 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 Q2KDT2
- Elsewhere: RCSB PDB 5TSD · PDBe 5TSD · UniProt Q2KDT2
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