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Crystal structure of hydroquinone 1,2-dioxygenase pnpcd in complex with CD2+ and 4-hydroxybenzonitrile

Analyse Crystal structure of hydroquinone 1,2-dioxygenase pnpcd in complex with CD2+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZXA
Type: protein
Length: 1,948 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydroquinone dioxygenase small subunit; Hydroquinone dioxygenase large subunit
UniProt: C1I210, C1I209
Ligands: H8N, CD
Pockets: 18 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Hydroquinone dioxygenase small subunit	protein	163	9% helix, 49% strand	C1I210
W, X, Y, Z	Hydroquinone dioxygenase large subunit	protein	324	17% helix, 35% strand	C1I209

Ligands and binding sites

H8N · 4-hydroxybenzonitrile · ligand · 4 copies · chains W, X, Y, Z
CD · Cadmium ion · metal · 4 copies · chains W, X, Y, Z

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

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	978	0.87	0.88	103	empty
2	952	0.86	0.88	105	empty
3	88	0.75	0.96	26	H8N
4	57	0.72	0.97	17	H8N
5	56	0.72	0.97	16	H8N

Interfaces

12 interfaces between chains.

D–Z · 3019 Å² buried · 55 hydrogen bonds · protein-protein
A–W · 3000 Å² buried · 48 hydrogen bonds · protein-protein
C–Y · 2985 Å² buried · 55 hydrogen bonds · protein-protein
B–X · 2968 Å² buried · 53 hydrogen bonds · protein-protein
W–X · 1166 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4ZXA · Crystal Structure of hydroqui 1,2-dioxygenase PnpCD in complex with Cd2+ and… · 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 C1I210
Every structure of UniProt C1I209
Elsewhere: RCSB PDB 4ZXA · PDBe 4ZXA · UniProt C1I210 · UniProt C1I209

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