MolNFT v1 · #132913 · protein
Methylmalonyl-CoA mutase, Y89F mutant, substrate complex
5REQ · Protein (methylmalonyl-CoA mutase alpha-subunit): “Methylmalonyl-CoA mutase, Y89F mutant, substrate complex”. X-ray diffraction, 3 ligands (SCD, MCD, B12), 20 pockets (best druggability 0.90). MolNFT v1 #132913 on GenesisL1: 3D…
- PDB
- 5REQ
- Type
- protein
- Length
- 2,688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (methylmalonyl-CoA mutase alpha-subunit); Protein (methylmalonyl-CoA mutase…
- EC
- 5.4.99.2
- UniProt
- P11653, P11652
- Ligands
- SCD, MCD, 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 alpha-subunit) (EC 5.4.99.2) | protein | 725 | 51% helix, 10% strand | P11653 |
| B, D | Protein (methylmalonyl-CoA mutase beta-subunit) (EC 5.4.99.2) | protein | 619 | 48% helix, 12% strand | P11652 |
Ligands and binding sites
- SCD · Succinyl(carbadethia)-coenzyme A · ligand · 2 copies · chains A, B, C, D
- MCD · Methylmalonyl(carbadethia)-coenzyme A · ligand · 2 copies · chains A, B, C, D
- B12 · Cobalamin · ligand · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.90 | 0.93 | 132 | SCD, MCD, B12 |
| 2 | 1170 | 0.89 | 0.91 | 124 | B12 |
| 3 | 1040 | 0.75 | 0.78 | 92 | empty |
| 4 | 263 | 0.69 | 0.85 | 33 | empty |
| 5 | 92 | 0.68 | 0.92 | 24 | SCD, MCD |
Interfaces
2 interfaces between chains.
- C–D · 5363 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 5345 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 5REQ · Methylmalonyl-COA MUTASE, Y89F Mutant, 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 5REQ · PDBe 5REQ · UniProt P11653 · UniProt P11652
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