MolNFT v1 · #48128 · protein + DNA

Helicase product complex

2PJR · DNA (5'-D(*TP*TP*TP*TP*T)-3'): “Helicase product complex”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.77). MolNFT v1 #48128 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PJR
Type: protein + DNA
Length: 1,293 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*TP*TP*TP*TP*T)-3'); DNA (5'-D(*GP*C)-3'); DNA (5'-D(*AP*CP*TP*GP*C)-3')…
EC: 3.6.1.-
UniProt: P56255
Ligands: SO4
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 52% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'-D(TPTPTPTP*T)-3')	dna	5	—	—
H	DNA (5'-D(GPC)-3')	dna	2	—	—
I	DNA (5'-D(APCPTPGP*C)-3')	dna	5	—	—
A	Protein (helicase pcra) (EC 3.6.1.-)	protein	542	55% helix, 10% strand	P56255
B, G	Protein (helicase pcra) (EC 3.6.1.-)	protein	95	27% helix, 32% strand	P56255
F	Protein (helicase pcra) (EC 3.6.1.-)	protein	544	52% helix, 10% strand	P56255

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains F, G, A, B

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1101	0.77	0.79	104	SO4
2	907	0.75	0.79	86	SO4
3	897	0.73	0.77	86	empty
4	533	0.69	0.79	38	empty
5	581	0.69	0.78	35	empty

Interfaces

10 interfaces between chains.

A–B · 3762 Å² buried · 64 hydrogen bonds · protein-protein
F–G · 3618 Å² buried · 67 hydrogen bonds · protein-protein
C–A · 777 Å² buried · 16 hydrogen bonds · protein-nucleic
D–F · 752 Å² buried · 14 hydrogen bonds · protein-nucleic
A–F · 641 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2PJR · Helicase product complex · the same entry in another collection · chain G against G, TM-score 1.00
P56255 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase pcra (P56255) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P56255
Elsewhere: RCSB PDB 2PJR · PDBe 2PJR · UniProt P56255

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.