Research workbench
Crystal structure of human methylmalonyl-CoA epimerase (mcee) P.ARG143CYS variant
Analyse Crystal structure of human methylmalonyl-CoA epimerase (mcee) P.ARG143CYS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QH4
- Type
- protein
- Length
- 534 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
- 11 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Methylmalonyl-CoA epimerase, mitochondrial (EC 5.1.99.1) | protein | 138 | 25% helix, 38% strand | Q96PE7 |
| A | Methylmalonyl-CoA epimerase, mitochondrial (EC 5.1.99.1) | protein | 131 | 25% helix, 39% strand | Q96PE7 |
| B | Methylmalonyl-CoA epimerase, mitochondrial (EC 5.1.99.1) | protein | 131 | 26% helix, 40% strand | Q96PE7 |
| D | Methylmalonyl-CoA epimerase, mitochondrial (EC 5.1.99.1) | protein | 134 | 25% helix, 39% strand | Q96PE7 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.62 | 0.77 | 47 | empty |
| 2 | 115 | 0.60 | 0.86 | 22 | empty |
| 3 | 176 | 0.57 | 0.80 | 24 | CO |
| 4 | 155 | 0.56 | 0.81 | 25 | CO |
| 5 | 143 | 0.54 | 0.81 | 23 | CO |
Interfaces
5 interfaces between chains.
- C–A · 1639 Ų buried · 21 hydrogen bonds · protein-protein
- C–B · 241 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 205 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 197 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 156 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6QH4 · Crystal structure of human Methylmalonyl-CoA epimerase (MCEE) p.Arg143Cys variant · the same entry in another collection · chain D against D, TM-score 1.00
- Q96PE7 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA epimerase, mitochondrial (Q96PE7) · a predicted model of the same protein · chain B 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 Q96PE7
- Elsewhere: RCSB PDB 6QH4 · PDBe 6QH4 · UniProt Q96PE7
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