MolNFT v1 · #139476 · protein

Isoaspartyl dipeptidase from colwellia psychrerythraea strain 34H

5XGW: “Isoaspartyl dipeptidase from colwellia psychrerythraea strain 34H”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.67). MolNFT v1 #139476 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XGW
Type: protein
Length: 748 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isoaspartyl dipeptidase
EC: 3.4.19.-
UniProt: Q484B6
Ligands: ZN
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Isoaspartyl dipeptidase (EC 3.4.19.-)	protein	374	30% helix, 29% strand	Q484B6

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

5 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	881	0.67	0.74	79	empty
2	182	0.52	0.78	32	empty
3	153	0.47	0.77	34	empty
4	57	0.33	0.77	15	empty
5	50	0.26	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 1262 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5XGW · Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H · 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 Q484B6
Elsewhere: RCSB PDB 5XGW · PDBe 5XGW · UniProt Q484B6

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