MolNFT v1 · #32875 · protein
2.01 ångström X-ray crystal structure of a mixed disulfide between coenzyme M and NADPH-dependent oxidoreductase 2- ketopropyl coenzyme M carboxylase
2C3C · 2-oxopropyl-com reductase: “2.01 ångström X-ray crystal structure of a mixed disulfide between coenzyme M and NADPH-dependent…”. X-ray diffraction, 4 ligands (COM, FAD, ACN), 11 pockets (best druggability 0.80). MolNFT v1 #32875 on…
- PDB
- 2C3C
- 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
- EC
- 1.8.1.5
- UniProt
- Q56839
- Ligands
- COM, FAD, ACN, NAP
- 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 (EC 1.8.1.5) | protein | 522 | 33% helix, 24% strand | Q56839 |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ACN · Acetone · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · 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 | 125 | 0.80 | 0.97 | 28 | ACN, COM |
| 2 | 122 | 0.80 | 0.97 | 27 | COM, ACN |
| 3 | 745 | 0.79 | 0.83 | 86 | FAD, NAP |
| 4 | 845 | 0.79 | 0.82 | 105 | FAD, NAP |
| 5 | 104 | 0.41 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4880 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 2C3C · 2.01 Angstrom X-ray crystal structure of a mixed disulfide between coenzyme M and… · 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 2C3C · PDBe 2C3C · UniProt Q56839
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