MolNFT v1 · #77704 · protein
Crystal structure of human methylmalonyl-CoA epimerase, mcee
3RMU · Methylmalonyl-CoA epimerase, mitochondrial: “Crystal structure of human methylmalonyl-CoA epimerase, mcee”. X-ray diffraction, 1 ligand (CO), 10 pockets (best druggability 0.70). MolNFT v1 #77704 on GenesisL1: 3D structure, binding…
- PDB
- 3RMU
- Type
- protein
- Length
- 536 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonyl-CoA epimerase, mitochondrial
- EC
- 5.1.99.1
- UniProt
- Q96PE7
- Ligands
- CO
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Methylmalonyl-CoA epimerase, mitochondrial (EC 5.1.99.1) | protein | 134 | 22% helix, 38% strand | Q96PE7 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B, D, C
- PG4 · Tetraethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.70 | 0.80 | 59 | EDO |
| 2 | 222 | 0.61 | 0.81 | 27 | CO, EDO |
| 3 | 187 | 0.60 | 0.82 | 27 | EDO |
| 4 | 194 | 0.60 | 0.82 | 27 | CO, EDO |
| 5 | 149 | 0.55 | 0.81 | 28 | CO |
Interfaces
5 interfaces between chains.
- C–D · 1675 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1624 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 194 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 177 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 136 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3RMU · Crystal structure of human Methylmalonyl-CoA epimerase, MCEE · the same entry in another collection · chain A against A, TM-score 1.00
- Q96PE7 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA epimerase, mitochondrial (Q96PE7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q96PE7
- Elsewhere: RCSB PDB 3RMU · PDBe 3RMU · UniProt Q96PE7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.