MolNFT v1 · #39742 · protein + DNA

Q44V mutant of homing endonuclease I-crei

2I3Q · 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*AP*CP*GP*TP*GP*AP*GP*TP*CP*AP…: “Q44V mutant of homing endonuclease I-crei”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.75). MolNFT v1 #39742 on GenesisL1: 3D structure, binding…

PDB: 2I3Q
Type: protein + DNA
Length: 352 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*AP*CP*GP*TP*GP*AP*GP*TP*CP*AP *GP*TP*TP*TP*CP*G)-3'…
EC: 3.1.-.-
UniProt: P05725
Ligands: CA
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(GPCPAPAPAPAPCPGPAPCPGPTPGPAPGPTPCPAP GPTPTPTPCPG)-3'	dna	24	—	—
D	5'-D(CPGPAPAPAPCPTPGPAPCPTPCPAPCPGPTPCPGP TPTPTPTPGPC)-3'	dna	24	—	—
A, B	DNA endonuclease I-crei (EC 3.1.-.-)	protein	152	55% helix, 20% strand	P05725

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains C, D, A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	117	0.75	0.95	31	empty
2	129	0.68	0.90	30	empty
3	64	0.61	0.90	13	empty
4	57	0.43	0.83	22	empty

Interfaces

6 interfaces between chains.

C–D · 1177 Å² buried · 105 hydrogen bonds · nucleic-nucleic
A–B · 992 Å² buried · 17 hydrogen bonds · protein-protein
C–A · 957 Å² buried · 24 hydrogen bonds · protein-nucleic
D–B · 945 Å² buried · 22 hydrogen bonds · protein-nucleic
C–B · 822 Å² buried · 15 hydrogen bonds · protein-nucleic

Compared structures

2I3Q · Q44V mutant of Homing Endonuclease I-CreI · the same entry in another collection · chain C against C, TM-score 1.00
P05725 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-crei (P05725) · a predicted model of the same protein · chain B 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 P05725
Elsewhere: RCSB PDB 2I3Q · PDBe 2I3Q · UniProt P05725

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.