Research workbench
Methylmalonyl-CoA mutase, non-productive CoA complex, in open conformation representing substrate-free state
Analyse Methylmalonyl-CoA mutase, non-productive CoA complex, in open conformation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2REQ
- Type
- protein
- Length
- 2,688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Propionibacterium freudenreichii subsp. shermanii
- Molecule
- Methylmalonyl-CoA mutase
- EC
- 5.4.99.2
- UniProt
- P11653, P11652
- Ligands
- COA, B12
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Methylmalonyl-CoA mutase (EC 5.4.99.2) | protein | 725 | 52% helix, 9% strand | P11653 |
| B, D | Methylmalonyl-CoA mutase (EC 5.4.99.2) | protein | 619 | 48% helix, 11% strand | P11652 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B, C, D
- B12 · Cobalamin · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.86 | 0.90 | 82 | B12 |
| 2 | 744 | 0.86 | 0.90 | 86 | B12 |
| 3 | 1038 | 0.71 | 0.75 | 69 | empty |
| 4 | 404 | 0.68 | 0.81 | 41 | empty |
| 5 | 410 | 0.67 | 0.80 | 44 | empty |
Interfaces
4 interfaces between chains.
- C–D · 5160 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 5159 Ų buried · 74 hydrogen bonds · protein-protein
- A–C · 172 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2REQ · Methylmalonyl-CoA mutase, non-productive CoA complex, in open conformation representing… · the same entry in another collection · chain A against A, TM-score 1.00
- P11652 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA mutase small subunit (P11652) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P11653 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA mutase large subunit (P11653) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P11653
- Every structure of UniProt P11652
- Elsewhere: RCSB PDB 2REQ · PDBe 2REQ · UniProt P11653 · UniProt P11652
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