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Cys-gly dipeptidase glij in complex with NI2+

Analyse Cys-gly dipeptidase glij in complex with NI2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NS1
Type: protein
Length: 381 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidase glij
EC: 3.4.13.19
UniProt: Q4WMJ8
Ligands: NI, CL
Pockets: 4 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidase glij (EC 3.4.13.19)	protein	381	50% helix, 12% strand	Q4WMJ8

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A
CL · Chloride ion · ion

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.36	0.76	19	empty
2	68	0.35	0.77	13	empty
3	60	0.35	0.78	10	empty
4	80	0.31	0.73	18	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5NS1 · Cys-Gly dipeptidase GliJ in complex with Ni2+ · the same entry in another collection · chain A against A, TM-score 1.00
Q4WMJ8 · AlphaFold monomer V2.0 prediction for dipeptidase glij (Q4WMJ8) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q4WMJ8
Elsewhere: RCSB PDB 5NS1 · PDBe 5NS1 · UniProt Q4WMJ8

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