MolNFT v1 · #77429 · protein
Methylmalonyl-CoA mutase, substrate-free state (poor quality structure)
3REQ: “Methylmalonyl-CoA mutase, substrate-free state (poor quality structure)”. X-ray diffraction, 2 ligands (B12, ADN), 15 pockets (best druggability 0.86). MolNFT v1 #77429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3REQ
- Type
- protein
- Length
- 1,345 residues
- Chains
- 2
- 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, ADN
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonyl-CoA mutase (EC 5.4.99.2) | protein | 725 | 47% helix, 9% strand | P11653 |
| B | Methylmalonyl-CoA mutase (EC 5.4.99.2) | protein | 620 | 45% helix, 12% strand | P11652 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.86 | 0.90 | 89 | B12 |
| 2 | 499 | 0.71 | 0.81 | 53 | empty |
| 3 | 95 | 0.68 | 0.92 | 24 | empty |
| 4 | 51 | 0.67 | 0.96 | 22 | empty |
| 5 | 299 | 0.65 | 0.81 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 5328 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 3REQ · Methylmalonyl-CoA mutase, substrate-free state (poor quality structure) · 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 0.99
- 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 0.93
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 3REQ · PDBe 3REQ · UniProt P11653 · UniProt P11652
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