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Crystal structure of seabream antiquitin and elucidation of its substrate specificity

Analyse Crystal structure of seabream antiquitin and elucidation of its substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2JG7
Type: protein
Length: 4,072 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antiquitin
UniProt: Q4KTQ7
Ligands: NAD
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Antiquitin	protein	509	41% helix, 21% strand	Q4KTQ7

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1107	0.87	0.88	78	empty
2	1110	0.86	0.87	81	empty
3	1128	0.86	0.87	81	empty
4	1116	0.86	0.87	67	empty
5	1168	0.86	0.87	82	empty

Interfaces

17 interfaces between chains.

A–B · 3803 Å² buried · 61 hydrogen bonds · protein-protein
E–F · 3790 Å² buried · 61 hydrogen bonds · protein-protein
G–H · 3774 Å² buried · 61 hydrogen bonds · protein-protein
C–D · 3770 Å² buried · 62 hydrogen bonds · protein-protein
E–H · 1070 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2JG7 · Crystal structure of Seabream Antiquitin and Elucidation of its substrate specificity · 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 Q4KTQ7
Elsewhere: RCSB PDB 2JG7 · PDBe 2JG7 · UniProt Q4KTQ7

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