MolNFT v1 · #59874 · protein

Crystal structure of L-talarate dehydratase from polaromonas sp. JS666 complexed with mg and L-glucarate

3CB3 · Mandelate RACEMASE/MUCONATE lactonizing enzyme: “Crystal structure of L-talarate dehydratase from polaromonas sp. JS666 complexed with mg and L-glucarate”. X-ray diffraction, 2 ligands (LGT, MG), 18 pockets (best druggability 0.87).…

PDB: 3CB3
Type: protein
Length: 1,449 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate RACEMASE/MUCONATE lactonizing enzyme
UniProt: Q12GE3
Ligands: LGT, MG
Pockets: 18 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	373	41% helix, 22% strand	Q12GE3
B	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	361	42% helix, 21% strand	Q12GE3
C	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	357	43% helix, 21% strand	Q12GE3
D	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	358	42% helix, 21% strand	Q12GE3

Ligands and binding sites

LGT · L-glucaric acid · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	900	0.87	0.89	90	empty
2	536	0.77	0.84	52	LGT
3	372	0.76	0.86	50	empty
4	153	0.69	0.89	27	MG
5	247	0.64	0.82	26	LGT

Interfaces

5 interfaces between chains.

A–D · 1259 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1152 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 965 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 434 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 426 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3CB3 · Crystal structure of L-Talarate dehydratase from Polaromonas sp. JS666 complexed with Mg… · 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 Q12GE3
Elsewhere: RCSB PDB 3CB3 · PDBe 3CB3 · UniProt Q12GE3

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