MolNFT v1 · #54229 · protein
Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin
2XIJ · Methylmalonyl-CoA mutase, mitochondrial: “Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin”. X-ray diffraction, 3 ligands (5AD, B12, SO4), 9 pockets (best druggability 0.85). MolNFT v1 #54229 on…
- PDB
- 2XIJ
- Type
- protein
- Length
- 710 residues
- Chains
- 1
- 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
- 5AD, B12, SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonyl-CoA mutase, mitochondrial (EC 5.4.99.2) | protein | 710 | 53% helix, 9% strand | P22033 |
Ligands and binding sites
- 5AD · 5'-deoxyadenosine · ligand · chains A
- B12 · Cobalamin · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.85 | 0.88 | 91 | 5AD, EDO, B12 |
| 2 | 95 | 0.64 | 0.90 | 26 | empty |
| 3 | 187 | 0.57 | 0.80 | 38 | empty |
| 4 | 68 | 0.56 | 0.88 | 25 | empty |
| 5 | 60 | 0.50 | 0.86 | 16 | BTB |
Compared structures
- 2XIJ · Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin · 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 0.98
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 2XIJ · PDBe 2XIJ · UniProt P22033
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