MolNFT v1 · #40421 · protein + DNA

Crystal structure of uvrd-DNA-ADPMGF3 ternary complex

2IS6 · 5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP…: “Crystal structure of uvrd-DNA-ADPMGF3 ternary complex”. X-ray diffraction, 3 ligands (MGF, ADP, MG), 18 pockets (best druggability 0.81). MolNFT v1 #40421 on GenesisL1…

PDB: 2IS6
Type: protein + DNA
Length: 1,352 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP *TP*TP*GP*TP*TP*AP*T)-3'; DNA…
EC: 3.6.1.-
UniProt: P03018
Ligands: MGF, ADP, MG
Pockets: 18 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	5'-D(CPGPAPGPCPAPCPTPGPCPAPGPTPGPCPTPCPGP TPTPGPTPTPAP*T)-3'	dna	23	—	—
A	DNA helicase II (EC 3.6.1.-)	protein	654	53% helix, 13% strand	P03018
B	DNA helicase II (EC 3.6.1.-)	protein	652	53% helix, 13% strand	P03018

Ligands and binding sites

MGF · Trifluoromagnesate · ligand · 2 copies · chains A, B
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · chains A

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

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	731	0.81	0.85	80	empty
2	657	0.80	0.85	74	empty
3	306	0.74	0.87	43	empty
4	724	0.73	0.79	72	GOL
5	58	0.69	0.97	15	empty

Interfaces

5 interfaces between chains.

C–A · 1081 Å² buried · 26 hydrogen bonds · protein-nucleic
D–B · 1080 Å² buried · 28 hydrogen bonds · protein-nucleic
C–D · 828 Å² buried · 88 hydrogen bonds · nucleic-nucleic
D–A · 294 Å² buried · 3 hydrogen bonds · protein-nucleic
C–B · 195 Å² buried · 2 hydrogen bonds · protein-nucleic

Compared structures

2IS6 · Crystal structure of UvrD-DNA-ADPMgF3 ternary complex · the same entry in another collection · chain C against C, TM-score 1.00
P03018 · AlphaFold monomer V2.0 prediction for DNA helicase II (P03018) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P03018
Elsewhere: RCSB PDB 2IS6 · PDBe 2IS6 · UniProt P03018

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