MolNFT v1 · #40419 · protein + DNA

Crystal structure of uvrd-DNA-adpnp ternary complex

2IS4 · 25-mer: “Crystal structure of uvrd-DNA-adpnp ternary complex”. X-ray diffraction, 2 ligands (ANP, MG), 16 pockets (best druggability 0.80). MolNFT v1 #40419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2IS4
Type: protein + DNA
Length: 1,328 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 25-mer; DNA helicase II
EC: 3.6.1.-
UniProt: P03018
Ligands: ANP, MG
Pockets: 16 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	25-mer	dna	25	—	—
D	25-mer	dna	25	—	—
A	DNA helicase II (EC 3.6.1.-)	protein	646	51% helix, 13% strand	P03018
B	DNA helicase II (EC 3.6.1.-)	protein	632	51% helix, 14% strand	P03018

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

16 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	1186	0.80	0.82	99	empty
2	1107	0.77	0.80	92	empty
3	632	0.72	0.80	51	empty
4	177	0.67	0.87	28	empty
5	108	0.65	0.90	20	empty

Interfaces

5 interfaces between chains.

C–B · 1320 Å² buried · 31 hydrogen bonds · protein-nucleic
D–A · 1307 Å² buried · 25 hydrogen bonds · protein-nucleic
C–D · 837 Å² buried · 94 hydrogen bonds · nucleic-nucleic
D–B · 232 Å² buried · 2 hydrogen bonds · protein-nucleic
C–A · 220 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

2IS4 · Crystal structure of UvrD-DNA-ADPNP 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 0.96

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 2IS4 · PDBe 2IS4 · UniProt P03018

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