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Intron-encoded endonuclease I-ppoi complexed with DNA

Analyse Intron-encoded endonuclease I-ppoi complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1A73
Type: protein + DNA
Length: 366 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3'); DNA…
UniProt: Q94702
Ligands: ZN, MG
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E	DNA (5'- D(TPTPGPAPCPTPCPTPCPTPTPAP*A)-3')	dna	13	—	—
D, F	DNA (5'-D(PGPAPGPAPGPTPCPA)-3')	dna	8	—	—
A, B	Intron 3 (I-ppo) encoded endonuclease	protein	162	19% helix, 33% strand	Q94702

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains E, F, A, C, D, B

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

Pockets

6 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	95	0.64	0.90	30	empty
2	169	0.47	0.76	24	empty
3	137	0.43	0.76	24	empty
4	107	0.37	0.75	21	MG
5	81	0.30	0.73	15	empty

Interfaces

12 interfaces between chains.

A–B · 2539 Å² buried · 39 hydrogen bonds · protein-protein
C–A · 599 Å² buried · 5 hydrogen bonds · protein-nucleic
E–B · 595 Å² buried · 4 hydrogen bonds · protein-nucleic
D–B · 475 Å² buried · 13 hydrogen bonds · protein-nucleic
F–A · 470 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

1A73 · Intron-encoded endonuclease I-ppoi complexed with DNA · the same entry in another collection · chain E against E, TM-score 1.00
Q94702 · AlphaFold monomer V2.0 prediction for intron-encoded endonuclease I-ppoi (Q94702) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q94702
Elsewhere: RCSB PDB 1A73 · PDBe 1A73 · UniProt Q94702

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