Research workbench
2.15 ångström crystal structure of 2-ketopropyl coenzyme M oxidoreductase carboxylase with a coenzyme M disulfide bound at the active site
Analyse 2.15 ångström crystal structure of 2-ketopropyl coenzyme M oxidoreductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C3D
- 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
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxopropyl-com reductase (EC 1.8.1.5) | protein | 522 | 33% helix, 23% strand | Q56839 |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.81 | 0.97 | 27 | COM |
| 2 | 143 | 0.80 | 0.97 | 27 | COM |
| 3 | 961 | 0.80 | 0.81 | 106 | FAD |
| 4 | 745 | 0.80 | 0.83 | 84 | FAD |
| 5 | 125 | 0.42 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 4852 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2C3D · 2.15 Angstrom crystal structure of 2-ketopropyl coenzyme M oxidoreductase carboxylase… · 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 2C3D · PDBe 2C3D · UniProt Q56839
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