Research workbench
NADPH dependent 2-ketopropyl coenzyme M OXIDOREDUCTASE/CARBOXYLASE
Analyse NADPH dependent 2-ketopropyl coenzyme M OXIDOREDUCTASE/CARBOXYLASE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MOK
- Type
- protein
- Length
- 2,088 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF3
- EC
- 1.8.1.5
- UniProt
- Q56839
- Ligands
- FAD
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ORF3 (EC 1.8.1.5) | protein | 522 | 32% helix, 23% strand | Q56839 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.82 | 0.90 | 57 | empty |
| 2 | 414 | 0.81 | 0.89 | 57 | empty |
| 3 | 430 | 0.80 | 0.88 | 56 | empty |
| 4 | 456 | 0.80 | 0.87 | 58 | empty |
| 5 | 793 | 0.79 | 0.82 | 104 | FAD |
Interfaces
2 interfaces between chains.
- A–B · 4408 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 4373 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MOK · NADPH dependent 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 0.98
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 1MOK · PDBe 1MOK · UniProt Q56839
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