Research workbench
Methylmalonyl-CoA mutase, 3-carboxypropyl-CoA inhibitor complex
Analyse Methylmalonyl-CoA mutase, 3-carboxypropyl-CoA inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6REQ
- Type
- protein
- Length
- 2,692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (methylmalonyl-CoA mutase)
- EC
- 5.4.99.2
- UniProt
- P11653, P11652
- Ligands
- 3CP, B12
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (methylmalonyl-CoA mutase) (EC 5.4.99.2) | protein | 727 | 52% helix, 10% strand | P11653 |
| B, D | Protein (methylmalonyl-CoA mutase) (EC 5.4.99.2) | protein | 619 | 48% helix, 12% strand | P11652 |
Ligands and binding sites
- 3CP · 3-carboxypropyl-coenzyme A · ligand · 2 copies · chains A, B, C, D
- B12 · Cobalamin · ligand · 2 copies · chains A, C
- GOL · Glycerol · additive · 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 | 1134 | 0.90 | 0.92 | 121 | B12, GOL |
| 2 | 469 | 0.86 | 0.93 | 68 | GOL |
| 3 | 366 | 0.83 | 0.92 | 54 | B12 |
| 4 | 829 | 0.76 | 0.80 | 89 | empty |
| 5 | 102 | 0.71 | 0.93 | 24 | empty |
Interfaces
2 interfaces between chains.
- C–D · 5342 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 5330 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 6REQ · Methylmalonyl-CoA mutase, 3-carboxypropyl-CoA inhibitor complex · 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 1.00
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 6REQ · PDBe 6REQ · UniProt P11653 · UniProt P11652
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