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The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)

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PDB: 2NL8
Type: protein + DNA
Length: 135 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18-nt pen element of the SV40 DNA origin; Large T antigen
UniProt: P03070
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
W	18-nt pen element of the SV40 DNA origin	dna	18	—	—
A	Large T antigen	protein	117	27% helix, 34% strand	P03070

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	64	0.35	0.77	13	empty

Interfaces

1 interface between chains.

W–A · 339 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

2NL8 · The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp… · the same entry in another collection · chain W against W, TM-score 1.00

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 P03070
Elsewhere: RCSB PDB 2NL8 · PDBe 2NL8 · UniProt P03070

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