Research workbench
Methylmalonyl-CoA mutase substrate complex
Analyse Methylmalonyl-CoA mutase substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4REQ
- Type
- protein
- Length
- 2,690 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl-CoA mutase
- EC
- 5.4.99.2
- UniProt
- P11653, P11652
- Ligands
- B12, SCA, MCA, 5AD
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Methylmalonyl-CoA mutase (EC 5.4.99.2) | protein | 726 | 51% helix, 10% strand | P11653 |
| B, D | Methylmalonyl-CoA mutase (EC 5.4.99.2) | protein | 619 | 47% helix, 12% strand | P11652 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, C
- SCA · Succinyl-coenzyme A · ligand · 2 copies · chains A, B, C, D
- MCA · Methylmalonyl-coenzyme A · ligand · 2 copies · chains A, B, C, D
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
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 | 878 | 0.90 | 0.93 | 115 | B12, 5AD, GOL |
| 2 | 652 | 0.88 | 0.92 | 87 | B12, 5AD |
| 3 | 214 | 0.81 | 0.95 | 31 | GOL |
| 4 | 778 | 0.76 | 0.80 | 84 | empty |
| 5 | 392 | 0.69 | 0.82 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5364 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 5363 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 4REQ · Methylmalonyl-COA Mutase substrate 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 4REQ · PDBe 4REQ · UniProt P11653 · UniProt P11652
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