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Crystal structure of the replication termination protein in complex with a pseudosymmetric 21MER B-site DNA

Analyse Crystal structure of the replication termination protein in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DPU
Type: protein + DNA
Length: 136 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(P*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'; 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*T)-3'…
UniProt: P68732
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	5'-D(PAPTPGPTPTPCPAPTPAPG)-3'	dna	10	—	—
E	5'-D(CPTPAPTPGPAPAPCPAPTP*T)-3'	dna	11	—	—
A	Replication termination protein	protein	115	53% helix, 5% strand	P68732

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	80	0.39	0.78	12	empty

Interfaces

3 interfaces between chains.

D–E · 473 Å² buried · 46 hydrogen bonds · nucleic-nucleic
E–A · 447 Å² buried · 9 hydrogen bonds · protein-nucleic
D–A · 417 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

2DPU · Crystal structure of the replication termination protein in complex with a… · the same entry in another collection · chain D against D, 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 P68732
Elsewhere: RCSB PDB 2DPU · PDBe 2DPU · UniProt P68732

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