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Crystal structure of uvrd-DNA binary complex

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

PDB: 2IS2
Type: protein + DNA
Length: 1,350 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 33-mer; DNA helicase II
EC: 3.6.1.-
UniProt: P03018
Pockets: 15 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	33-mer	dna	33	—	—
A, B	DNA helicase II (EC 3.6.1.-)	protein	642	51% helix, 13% strand	P03018

Ligands and binding sites

GOL · Glycerol · additive · chains A
FMT · Formic acid · additive · chains A

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.81	0.83	106	empty
2	831	0.79	0.82	84	FMT
3	315	0.75	0.87	49	empty
4	431	0.69	0.81	32	empty
5	508	0.66	0.78	44	empty

Interfaces

5 interfaces between chains.

C–D · 1276 Å² buried · 128 hydrogen bonds · nucleic-nucleic
D–B · 1238 Å² buried · 31 hydrogen bonds · protein-nucleic
C–A · 1206 Å² buried · 32 hydrogen bonds · protein-nucleic
D–A · 345 Å² buried · 7 hydrogen bonds · protein-nucleic
C–B · 342 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

2IS2 · Crystal structure of UvrD-DNA binary complex · the same entry in another collection · chain A against A, 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 0.95

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 2IS2 · PDBe 2IS2 · UniProt P03018

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