MolNFT v1 · #4505 · protein

Crystal structure of an archaeal intein-encoded homing endonuclease pi-pfui

1DQ3: “Crystal structure of an archaeal intein-encoded homing endonuclease pi-pfui”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.54). MolNFT v1 #4505 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DQ3
Type: protein
Length: 454 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endonuclease
UniProt: P95484
Ligands: ZN
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Endonuclease	protein	454	33% helix, 35% strand	P95484

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	173	0.54	0.79	26	empty
2	101	0.48	0.81	22	empty
3	70	0.35	0.77	19	empty
4	78	0.31	0.74	18	empty
5	69	0.29	0.74	21	empty

Compared structures

1DQ3 · Crystal structure of an archaeal intein-encoded homing endonuclease pi-pfui · 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 P95484
Elsewhere: RCSB PDB 1DQ3 · PDBe 1DQ3 · UniProt P95484

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