MolNFT v1 · #153840 · protein

Zhd complex with hydrolyzed beta-zol

6JRD · Zearalenone hydrolase: “Zhd complex with hydrolyzed beta-zol”. X-ray diffraction, 2 ligands (C1U, K), 2 pockets (best druggability 0.75). MolNFT v1 #153840 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JRD
Type: protein
Length: 537 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Zearalenone hydrolase
UniProt: Q8NKB0
Ligands: C1U, K
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Zearalenone hydrolase	protein	268	51% helix, 18% strand	Q8NKB0
B	Zearalenone hydrolase	protein	269	51% helix, 18% strand	Q8NKB0

Ligands and binding sites

C1U · 2-[(~{E},6~{S},10~{S})-6,10-bis(oxidanyl)undec-1-enyl]-4,6-bis(oxidanyl)benzoic acid · ligand · 2 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 8 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	313	0.75	0.86	34	C1U, GOL
2	274	0.74	0.87	33	C1U, GOL

Interfaces

1 interface between chains.

A–B · 638 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6JRD · ZHD complex with hydrolyzed beta-ZOL · 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 Q8NKB0
Elsewhere: RCSB PDB 6JRD · PDBe 6JRD · UniProt Q8NKB0

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