MolNFT v1 · #23440 · protein + DNA

Y33C mutant of homing endonuclease I-crei

1U0C · 5'-D(*GP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP…: “Y33C mutant of homing endonuclease I-crei”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.70). MolNFT v1 #23440 on GenesisL1: 3D structure, binding…

PDB: 1U0C
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*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*AP*CP*G)-3'…
EC: 3.1.-.-
UniProt: P05725
Ligands: MG
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(GPCPTPAPAPAPCPGPTPCPGPTPGPAPGPAPCPAP GPTPTPAPCPG)-3'	dna	24	—	—
D	5'-D(CPGPTPAPAPCPTPGPTPCPTPCPAPCPGPAPCPGP TPTPTPAPGPC)-3'	dna	24	—	—
A, B	DNA endonuclease I-crei (EC 3.1.-.-)	protein	152	52% helix, 20% strand	P05725

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains C, D, A, B

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

Pockets

3 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	71	0.70	0.96	22	empty
2	84	0.62	0.89	16	empty
3	56	0.42	0.83	19	empty

Interfaces

6 interfaces between chains.

C–D · 1191 Å² buried · 100 hydrogen bonds · nucleic-nucleic
A–B · 994 Å² buried · 15 hydrogen bonds · protein-protein
C–A · 984 Å² buried · 28 hydrogen bonds · protein-nucleic
D–B · 889 Å² buried · 20 hydrogen bonds · protein-nucleic
C–B · 876 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

1U0C · Y33C 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 A 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 1U0C · PDBe 1U0C · UniProt P05725

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