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Crystal structure of human methylmalonyl-CoA epimerase, mcee

Analyse Crystal structure of human methylmalonyl-CoA epimerase, mcee in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1624 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 194 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 177 Å² buried · 1 hydrogen bond · protein-protein
A–C · 136 Å² 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

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