MolNFT v1 · #22586 · protein + DNA

I-CREI(Q47E)/DNA complex

1T9J · 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP…: “I-CREI(Q47E)/DNA complex”. X-ray diffraction, 4 pockets (best druggability 0.72). MolNFT v1 #22586 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1T9J
Type: protein + DNA
Length: 350 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*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*TP*CP*G)-3'…
EC: 3.1.-.-
UniProt: P05725
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 57% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(GPCPAPAPAPAPCPGPTPCPGPTPGPAPGPAPCPAP GPTPTPTPCPG)-3'	dna	24	—	—
D	5'-D(CPGPAPAPAPCPTPGPTPCPTPCPAPCPGPAPCPGP TPTPTPTPGPC)-3'	dna	24	—	—
A, B	DNA endonuclease I-crei (EC 3.1.-.-)	protein	151	57% helix, 21% strand	P05725

Pockets

4 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	85	0.72	0.95	24	empty
2	92	0.67	0.92	25	empty
3	53	0.43	0.84	21	empty
4	60	0.43	0.83	19	empty

Interfaces

6 interfaces between chains.

C–D · 1173 Å² buried · 97 hydrogen bonds · nucleic-nucleic
A–B · 983 Å² buried · 13 hydrogen bonds · protein-protein
C–A · 975 Å² buried · 26 hydrogen bonds · protein-nucleic
D–B · 966 Å² buried · 23 hydrogen bonds · protein-nucleic
C–B · 882 Å² buried · 15 hydrogen bonds · protein-nucleic

Compared structures

1T9J · I-CreI(Q47E)/DNA complex · 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 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 P05725
Elsewhere: RCSB PDB 1T9J · PDBe 1T9J · UniProt P05725

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