Research workbench
Crystal structure of F501H/H506E variant of 2-ketopropyl coenzyme M OXIDOREDUCTASE/CARBOXYLASE (2-kpcc) from xanthobacter autotrophicus
Analyse Crystal structure of F501H/H506E variant of 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
- 7MGN
- 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
- COM, FDA, MG
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% 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, 25% strand | Q56839 |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · 2 copies · chains A, B
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.79 | 0.98 | 27 | COM |
| 2 | 759 | 0.79 | 0.83 | 93 | FDA |
| 3 | 110 | 0.79 | 0.98 | 27 | COM |
| 4 | 767 | 0.79 | 0.82 | 90 | FDA |
| 5 | 111 | 0.39 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 4919 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7MGN · Crystal structure of F501H/H506E variant of 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 7MGN · PDBe 7MGN · UniProt Q56839
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