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Crystal structure of se-met methylmalonyl-CoA epimerase

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

PDB: 1JC4
Type: protein
Length: 579 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylmalonyl-CoA epimerase
EC: 5.1.99.1
UniProt: Q8VQN0
Ligands: SO4
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Methylmalonyl-CoA epimerase (EC 5.1.99.1)	protein	145	24% helix, 35% strand	Q8VQN0
B	Methylmalonyl-CoA epimerase (EC 5.1.99.1)	protein	144	23% helix, 36% strand	Q8VQN0

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D

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

Pockets

8 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	581	0.69	0.78	58	SO4
2	256	0.62	0.81	33	SO4
3	246	0.62	0.81	32	SO4
4	269	0.61	0.80	29	empty
5	258	0.57	0.78	34	SO4

Interfaces

3 interfaces between chains.

C–D · 1768 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1740 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 449 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

1JC4 · Crystal Structure of Se-Met Methylmalonyl-CoA Epimerase · the same entry in another collection · chain A 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 Q8VQN0
Elsewhere: RCSB PDB 1JC4 · PDBe 1JC4 · UniProt Q8VQN0

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