Research workbench
Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M OXIDOREDUCTASE/CARBOXYLASE
Analyse Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q6J
- Type
- protein
- Length
- 1,044 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxopropyl-com reductase, carboxylating
- EC
- 1.8.1.5
- UniProt
- Q56839
- Ligands
- NAP, FAD, BCT, ACN, KPC, COM, MG, CO2
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxopropyl-com reductase, carboxylating (EC 1.8.1.5) | protein | 522 | 33% helix, 24% strand | Q56839 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B
- ACN · Acetone · ligand · chains A, B
- KPC · (2-[2-ketopropylthio]ethanesulfonate · ligand · chains A, B
- COM · 1-thioethanesulfonic acid · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CO2 · Carbon dioxide · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.80 | 0.98 | 28 | ACN, BCT, COM |
| 2 | 773 | 0.79 | 0.83 | 93 | NAP, FAD |
| 3 | 117 | 0.79 | 0.97 | 26 | KPC, BCT, CO2 |
| 4 | 774 | 0.78 | 0.82 | 90 | NAP, FAD |
| 5 | 105 | 0.40 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4946 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 3Q6J · Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M… · the same entry in another collection · chain A against A, TM-score 1.00
- Q56839 · AlphaFold monomer V2.0 prediction for 2-oxopropyl-com reductase, carboxylating (Q56839) · 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 Q56839
- Elsewhere: RCSB PDB 3Q6J · PDBe 3Q6J · UniProt Q56839
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