Research workbench
Crystal structure of C-domain with CoA of baterial malonyl-CoA reductase
Analyse Crystal structure of C-domain with CoA 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
- 6K8T
- Type
- protein
- Length
- 1,324 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
- COA, SO4
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent EPIMERASE/DEHYDRATASE:SHORT-chain DEHYDROGENASE/REDUCTASE sdr | protein | 662 | 51% helix, 11% strand | A0A1A7BFR5 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.81 | 0.82 | 106 | COA, GOL |
| 2 | 1092 | 0.80 | 0.81 | 91 | COA, GOL |
| 3 | 130 | 0.79 | 0.97 | 24 | empty |
| 4 | 235 | 0.77 | 0.91 | 45 | empty |
| 5 | 244 | 0.75 | 0.89 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 3188 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 6K8T · Crystal structure of C-domain with CoA of baterial malonyl-CoA reductase · the same entry in another collection · chain B against B, 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 6K8T · PDBe 6K8T · UniProt A0A1A7BFR5
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