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Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from bacillus subtilis at 1.8 a resolution

Analyse Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GDQ
Type: protein
Length: 746 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yitf
UniProt: O06741
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yitf	protein	373	38% helix, 23% strand	O06741

Pockets

9 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	548	0.78	0.85	57	empty
2	187	0.61	0.83	28	empty
3	324	0.58	0.77	30	empty
4	142	0.56	0.82	30	empty
5	297	0.56	0.77	33	empty

Interfaces

1 interface between chains.

A–B · 1173 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2GDQ · Crystal structure of mandelate racemase/muconate lactonizing enzyme from Bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
O06741 · AlphaFold monomer V2.0 prediction for putative isomerase yitf (O06741) · a predicted model of the same protein · chain A 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 O06741
Elsewhere: RCSB PDB 2GDQ · PDBe 2GDQ · UniProt O06741

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