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Crystal structure of uvrd-DNA-SO4 complex

Analyse Crystal structure of uvrd-DNA-SO4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IS1
Type: protein + DNA
Length: 1,324 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*TP*TP*TP*TP*T)- 3'…
EC: 3.6.1.-
UniProt: P03018
Ligands: HG, SO4
Pockets: 13 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(GPCPAPGPTPGPCPTPCPGPTPTPTPTPTPTP*T)- 3'	dna	16	—	—
D, F	5'-D(CPGPAPGPCPAPCPTPGPC)-3'	dna	10	—	—
E	5'-D(GPCPAPGPTPGPCPTPCPGPTPTPTPTPTPTP*T)- 3'	dna	15	—	—
A	DNA helicase II (EC 3.6.1.-)	protein	649	51% helix, 13% strand	P03018
B	DNA helicase II (EC 3.6.1.-)	protein	624	50% helix, 12% strand	P03018

Ligands and binding sites

HG · Mercury (II) ion · metal · 5 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	979	0.81	0.82	91	SO4, GOL
2	1034	0.78	0.80	88	SO4, GOL
3	630	0.71	0.79	83	empty
4	80	0.70	0.94	25	empty
5	747	0.68	0.76	48	empty

Interfaces

14 interfaces between chains.

C–A · 994 Å² buried · 18 hydrogen bonds · protein-nucleic
E–B · 808 Å² buried · 17 hydrogen bonds · protein-nucleic
E–F · 478 Å² buried · 48 hydrogen bonds · nucleic-nucleic
C–D · 468 Å² buried · 52 hydrogen bonds · nucleic-nucleic
F–A · 301 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

2IS1 · Crystal structure of UvrD-DNA-SO4 complex · the same entry in another collection · chain B against B, TM-score 1.00
P03018 · AlphaFold monomer V2.0 prediction for DNA helicase II (P03018) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 2IS1 · PDBe 2IS1 · UniProt P03018

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