Research workbench
Crystal structure of C-domain with NADP of baterial malonyl-CoA reductase
Analyse Crystal structure of C-domain with NADP of baterial malonyl-CoA reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K8U
- Type
- protein
- Length
- 1,322 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
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent EPIMERASE/DEHYDRATASE:SHORT-chain DEHYDROGENASE/REDUCTASE sdr | protein | 662 | 50% helix, 11% strand | A0A1A7BFR5 |
| B | NAD-dependent EPIMERASE/DEHYDRATASE:SHORT-chain DEHYDROGENASE/REDUCTASE sdr | protein | 660 | 49% helix, 11% strand | A0A1A7BFR5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 15 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.80 | 0.81 | 91 | NAP, SO4 |
| 2 | 123 | 0.79 | 0.97 | 23 | empty |
| 3 | 1169 | 0.79 | 0.81 | 98 | NAP, SO4 |
| 4 | 220 | 0.75 | 0.90 | 33 | empty |
| 5 | 234 | 0.74 | 0.89 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 3208 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 6K8U · Crystal structure of C-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 6K8U · PDBe 6K8U · UniProt A0A1A7BFR5
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