MolNFT v1 · #154364 · protein
Crystal structure of N-domain with NADP of baterial malonyl-CoA reductase
6K8W · NAD-dependent EPIMERASE/DEHYDRATASE:SHORT-chain…: “Crystal structure of N-domain with NADP of baterial malonyl-CoA reductase”. X-ray diffraction, 2 ligands (NAP, SO4), 10 pockets (best druggability 0.82). MolNFT v1 #154364 on…
- PDB
- 6K8W
- Type
- protein
- Length
- 1,090 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent EPIMERASE/DEHYDRATASE:SHORT-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- A0A1A7BFR5
- Ligands
- NAP, SO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent EPIMERASE/DEHYDRATASE:SHORT-chain DEHYDROGENASE/REDUCTASE sdr | protein | 545 | 46% helix, 13% strand | A0A1A7BFR5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.82 | 0.83 | 120 | empty |
| 2 | 517 | 0.73 | 0.82 | 46 | NAP |
| 3 | 79 | 0.73 | 0.96 | 27 | empty |
| 4 | 94 | 0.72 | 0.95 | 28 | empty |
| 5 | 543 | 0.71 | 0.80 | 44 | NAP |
Interfaces
1 interface between chains.
- A–B · 2291 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6K8W · Crystal structure of N-domain with NADP of baterial malonyl-CoA reductase · 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 A0A1A7BFR5
- Elsewhere: RCSB PDB 6K8W · PDBe 6K8W · UniProt A0A1A7BFR5
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