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Co-crystal of bacteriophage T4 RNase H with a fork DNA substrate

Analyse Co-crystal of bacteriophage T4 RNase H with a fork DNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IHN
Type: protein + DNA
Length: 333 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*TP*AP*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*CP*C) -3'…
EC: 3.1.26.4
UniProt: P13319
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(CPTPAPAPCPTPTPTPGPAPGPGPCPAPGPAPCPC) -3'	dna	17	—	—
D	5'-D(GPGPTPCPTPGPCPCPTPCPAPAPGPAPCPGPGPTP APGPTPCPAPA)-3'	dna	17	—	—
A	Ribonuclease H (EC 3.1.26.4)	protein	299	49% helix, 9% strand	P13319

Pockets

3 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	951	0.77	0.80	66	empty
2	105	0.37	0.74	17	empty
3	81	0.32	0.74	16	empty

Interfaces

3 interfaces between chains.

D–A · 1242 Å² buried · 28 hydrogen bonds · protein-nucleic
C–A · 994 Å² buried · 11 hydrogen bonds · protein-nucleic
C–D · 533 Å² buried · 58 hydrogen bonds · nucleic-nucleic

Compared structures

2IHN · Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate · the same entry in another collection · chain C against C, 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 P13319
Elsewhere: RCSB PDB 2IHN · PDBe 2IHN · UniProt P13319

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