MolNFT v1 · #23441 · protein + DNA

Y33H mutant of homing endonuclease I-crei

1U0D · 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP…: “Y33H mutant of homing endonuclease I-crei”. X-ray diffraction, 4 pockets (best druggability 0.75). MolNFT v1 #23441 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1U0D
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*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*CP*CP*G)-3'…
EC: 3.1.-.-
UniProt: P05725
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(GPCPGPAPAPAPCPGPTPCPGPTPGPAPGPAPCPAP GPTPTPCPCPG)-3'	dna	24	—	—
D	5'-D(CPGPGPAPAPCPTPGPTPCPTPCPAPCPGPAPCPGP TPTPTPCPGPC)-3'	dna	24	—	—
A, B	DNA endonuclease I-crei (EC 3.1.-.-)	protein	152	49% helix, 20% strand	P05725

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	99	0.75	0.96	27	empty
2	130	0.68	0.90	29	empty
3	90	0.54	0.86	25	empty
4	81	0.52	0.85	26	empty

Interfaces

6 interfaces between chains.

C–D · 1165 Å² buried · 88 hydrogen bonds · nucleic-nucleic
C–A · 985 Å² buried · 20 hydrogen bonds · protein-nucleic
A–B · 985 Å² buried · 13 hydrogen bonds · protein-protein
D–B · 977 Å² buried · 22 hydrogen bonds · protein-nucleic
D–A · 822 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

1U0D · Y33H 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 0.98

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 P05725
Elsewhere: RCSB PDB 1U0D · PDBe 1U0D · UniProt P05725

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