MolNFT v1 · #54235 · protein
Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin and malonyl-CoA
2XIQ · Methylmalonyl-CoA mutase, mitochondrial: “Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin and malonyl-CoA”. X-ray diffraction, 3 ligands (B12, 5AD, MLC), 13 pockets (best druggability 0.89).…
- PDB
- 2XIQ
- Type
- protein
- Length
- 1,427 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl-CoA mutase, mitochondrial
- EC
- 5.4.99.2
- UniProt
- P22033
- Ligands
- B12, 5AD, MLC
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonyl-CoA mutase, mitochondrial (EC 5.4.99.2) | protein | 714 | 54% helix, 10% strand | P22033 |
| B | Methylmalonyl-CoA mutase, mitochondrial (EC 5.4.99.2) | protein | 713 | 53% helix, 10% strand | P22033 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, B
- MLC · Malonyl-coenzyme A · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.89 | 0.90 | 126 | B12, 5AD, MLC |
| 2 | 1134 | 0.88 | 0.90 | 120 | B12, 5AD, MLC |
| 3 | 801 | 0.86 | 0.89 | 118 | empty |
| 4 | 96 | 0.62 | 0.89 | 25 | empty |
| 5 | 81 | 0.60 | 0.89 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1457 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2XIQ · Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin and… · the same entry in another collection · chain A against A, TM-score 1.00
- P22033 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA mutase, mitochondrial (P22033) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P22033
- Elsewhere: RCSB PDB 2XIQ · PDBe 2XIQ · UniProt P22033
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.