Research workbench

L-ala-D/L-glu epimerase

Analyse L-ala-D/L-glu epimerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JPM
Type: protein
Length: 1,434 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-ala-D/L-glu epimerase
UniProt: O34508
Ligands: MG
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	L-ala-D/L-glu epimerase	protein	359	41% helix, 26% strand	O34508
C, D	L-ala-D/L-glu epimerase	protein	358	40% helix, 26% strand	O34508

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · chains A, C

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	708	0.83	0.87	61	empty
2	796	0.82	0.85	76	empty
3	593	0.73	0.80	47	empty
4	561	0.72	0.80	40	empty
5	762	0.71	0.77	80	GOL

Interfaces

4 interfaces between chains.

A–B · 1327 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1322 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 344 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 218 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1JPM · L-Ala-D/L-Glu Epimerase · the same entry in another collection · chain D against D, TM-score 1.00
O34508 · AlphaFold monomer V2.0 prediction for L-ala-D/L-glu epimerase (O34508) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 O34508
Elsewhere: RCSB PDB 1JPM · PDBe 1JPM · UniProt O34508

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