MolNFT v1 · #128495 · protein

Cys-gly dipeptidase glij in complex with FE3+

5NRY: “Cys-gly dipeptidase glij in complex with FE3+”. X-ray diffraction, 2 ligands (FE, CL), 3 pockets (best druggability 0.34). MolNFT v1 #128495 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NRY
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: FE, CL
Pockets: 3 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptidase glij (EC 3.4.13.19)	protein	381	51% helix, 12% strand	Q4WMJ8

Ligands and binding sites

FE · Fe (III) ion · metal · 2 copies · chains A
CL · Chloride ion · ion · 3 copies · chains A

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

Pockets

3 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	73	0.34	0.76	17	empty
2	59	0.34	0.77	14	empty
3	71	0.30	0.74	19	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5NRY · Cys-Gly dipeptidase GliJ in complex with Fe3+ · 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 5NRY · PDBe 5NRY · UniProt Q4WMJ8

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