Research workbench

Bh-RNASEH:TCDA-DNA complex

Analyse Bh-RNASEH:TCDA-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OPJ
Type: protein + DNA
Length: 289 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease H; 5'-D(*CP*GP*CP*GP*AP*(TCY)P*TP*TP*CP*GP*CP*G)-3'
EC: 3.1.26.4
UniProt: Q9KEI9
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease H (EC 3.1.26.4)	protein	133	35% helix, 26% strand	Q9KEI9
B, D	5'-D(CPGPCPGPAP(TCY)PTPTPCPGPCPG)-3'	dna	12	—	—
C	Ribonuclease H (EC 3.1.26.4)	protein	132	36% helix, 27% strand	Q9KEI9

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	387	0.59	0.76	35	empty
2	132	0.41	0.75	21	empty
3	61	0.35	0.77	10	empty
4	62	0.31	0.75	11	GOL
5	59	0.26	0.73	17	GOL

Interfaces

4 interfaces between chains.

C–D · 402 Å² buried · 10 hydrogen bonds · protein-nucleic
A–B · 391 Å² buried · 12 hydrogen bonds · protein-nucleic
A–C · 147 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 139 Å² buried · 1 hydrogen bond · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

4OPJ · Bh-RNaseH:tcdA-DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9KEI9 · AlphaFold monomer V2.0 prediction for ribonuclease H (Q9KEI9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9KEI9
Elsewhere: RCSB PDB 4OPJ · PDBe 4OPJ · UniProt Q9KEI9

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