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Crystal structure of methylmalonyl CoA decarboxylase

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

PDB: 1EF8
Type: protein
Length: 759 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylmalonyl CoA decarboxylase
EC: 4.1.1.41
UniProt: P52045
Ligands: NI
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methylmalonyl CoA decarboxylase (EC 4.1.1.41)	protein	256	46% helix, 16% strand	P52045
B	Methylmalonyl CoA decarboxylase (EC 4.1.1.41)	protein	253	46% helix, 16% strand	P52045
C	Methylmalonyl CoA decarboxylase (EC 4.1.1.41)	protein	250	47% helix, 16% strand	P52045

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	529	0.83	0.89	57	NI
2	247	0.64	0.81	44	empty
3	332	0.63	0.79	42	empty
4	301	0.61	0.78	44	empty
5	270	0.53	0.75	30	empty

Interfaces

3 interfaces between chains.

B–C · 1745 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 1722 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1684 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

1EF8 · Crystal structure of methylmalonyl CoA decarboxylase · the same entry in another collection · chain A against A, TM-score 1.00
P52045 · AlphaFold monomer V2.0 prediction for methylmalonyl-CoA decarboxylase (P52045) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 P52045
Elsewhere: RCSB PDB 1EF8 · PDBe 1EF8 · UniProt P52045

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