Research workbench

Homing ENDONUCLEASE/DNA complex

Analyse Homing ENDONUCLEASE/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IPP
Type: protein + DNA
Length: 366 residues
Chains: 4
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*AP*GP*AP*GP*AP*GP*TP *CP*A)-3')…
UniProt: Q94702
Ligands: CD, MG
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'- D(TPTPGPAPCPTPCPTPCPTPTPAPAPGPAPGPAPGPTP CP*A)-3')	dna	21	—	—
A, B	Intron-encoded endonuclease I-ppoi	protein	162	19% helix, 30% strand	Q94702

Ligands and binding sites

CD · Cadmium ion · metal · 4 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains D, A, C, 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	125	0.64	0.87	32	empty
2	176	0.47	0.76	24	empty
3	148	0.43	0.76	25	empty
4	83	0.31	0.73	16	empty
5	71	0.28	0.73	13	empty

Interfaces

6 interfaces between chains.

A–B · 2538 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 941 Å² buried · 88 hydrogen bonds · nucleic-nucleic
C–B · 608 Å² buried · 16 hydrogen bonds · protein-nucleic
C–A · 607 Å² buried · 5 hydrogen bonds · protein-nucleic
D–A · 601 Å² buried · 16 hydrogen bonds · protein-nucleic

Compared structures

1IPP · Homing ENDONUCLEASE/DNA complex · the same entry in another collection · chain C against C, 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 1IPP · PDBe 1IPP · UniProt Q94702

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