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Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)- tartaric acids

Analyse Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)- tartaric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZMY
Type: protein
Length: 2,233 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cis-epoxysuccinate hydrolase
UniProt: F1LJ99
Ligands: ZN
Pockets: 20 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Cis-epoxysuccinate hydrolase	protein	280	36% helix, 20% strand	F1LJ99
B, F, H	Cis-epoxysuccinate hydrolase	protein	279	36% helix, 20% strand	F1LJ99
C	Cis-epoxysuccinate hydrolase	protein	280	36% helix, 20% strand	F1LJ99
D, E	Cis-epoxysuccinate hydrolase	protein	278	36% helix, 20% strand	F1LJ99

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
TAR · D(-)-tartaric acid · additive · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 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	538	0.67	0.77	70	TAR
2	282	0.64	0.81	39	TAR
3	344	0.63	0.79	42	ZN, TAR
4	402	0.63	0.77	47	TAR
5	328	0.62	0.79	43	ZN, TAR

Interfaces

14 interfaces between chains.

C–D · 1739 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1721 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 1721 Å² buried · 31 hydrogen bonds · protein-protein
G–H · 1711 Å² buried · 31 hydrogen bonds · protein-protein
F–G · 898 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5ZMY · Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)-tartaric acids · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt F1LJ99
Elsewhere: RCSB PDB 5ZMY · PDBe 5ZMY · UniProt F1LJ99

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