MolNFT v1 · #22585 · protein + DNA

I-CREI(D20N)/DNA complex

1T9I · 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP…: “I-CREI(D20N)/DNA complex”. X-ray diffraction, 2 ligands (NA, CA), 4 pockets (best druggability 0.75). MolNFT v1 #22585 on GenesisL1: 3D structure, binding sites and…

PDB: 1T9I
Type: protein + DNA
Length: 356 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
Ligands: NA, CA
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 56% helix, 20% 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	DNA endonuclease I-crei (EC 3.1.-.-)	protein	153	56% helix, 20% strand	P05725
B	DNA endonuclease I-crei (EC 3.1.-.-)	protein	155	56% helix, 19% strand	P05725

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains C, D, A, B
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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.75	0.95	34	empty
2	120	0.69	0.91	26	empty
3	62	0.46	0.84	21	empty
4	53	0.45	0.85	20	empty

Interfaces

6 interfaces between chains.

C–D · 1171 Å² buried · 96 hydrogen bonds · nucleic-nucleic
C–A · 990 Å² buried · 29 hydrogen bonds · protein-nucleic
A–B · 980 Å² buried · 10 hydrogen bonds · protein-protein
D–B · 972 Å² buried · 24 hydrogen bonds · protein-nucleic
C–B · 854 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

1T9I · I-CreI(D20N)/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 B 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 1T9I · PDBe 1T9I · UniProt P05725

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