Research workbench
The crystal structure of methylmalonyl CoA decarboxylase complexed with 2S-carboxypropyl CoA
Analyse The crystal structure of methylmalonyl CoA decarboxylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EF9
- Type
- protein
- Length
- 261 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl CoA decarboxylase
- EC
- 4.1.1.41
- UniProt
- P52045
- Ligands
- 2CP
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonyl CoA decarboxylase (EC 4.1.1.41) | protein | 261 | 44% helix, 16% strand | P52045 |
Ligands and binding sites
- 2CP · 2-carboxypropyl-coenzyme A · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.66 | 0.83 | 39 | 2CP |
| 2 | 353 | 0.54 | 0.74 | 41 | empty |
| 3 | 151 | 0.50 | 0.79 | 18 | empty |
Compared structures
- 1EF9 · The crystal structure of methylmalonyl CoA decarboxylase complexed with 2S-carboxypropyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P52045 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA decarboxylase (P52045) · 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 P52045
- Elsewhere: RCSB PDB 1EF9 · PDBe 1EF9 · UniProt P52045
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