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Structure of LC11-RNase H1 isolated from compost by metagenomic approach: insight into the structural bases for unusual enzymatic properties of sto-RNase H1

Analyse Structure of LC11-RNase H1 isolated from compost by metagenomic approach… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U3G
Type: protein
Length: 560 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease H
EC: 3.1.26.4
UniProt: E0X767
Ligands: UNL, CL
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, B, C, A	Ribonuclease H (EC 3.1.26.4)	protein	140	47% helix, 30% strand	E0X767

Ligands and binding sites

UNL · Unknown ligand · ligand · chains A
CL · Chloride ion · ion · 2 copies · chains C, D, A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	753	0.71	0.77	54	empty
2	585	0.69	0.79	59	CL
3	73	0.35	0.76	16	empty

Interfaces

4 interfaces between chains.

D–A · 1174 Å² buried · 20 hydrogen bonds · protein-protein
D–B · 543 Å² buried · 3 hydrogen bonds · protein-protein
C–A · 268 Å² buried · 5 hydrogen bonds · protein-protein
D–C · 35 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3U3G · Structure of LC11-RNase H1 Isolated from Compost by Metagenomic Approach: Insight into… · the same entry in another collection · chain D against D, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt E0X767
Elsewhere: RCSB PDB 3U3G · PDBe 3U3G · UniProt E0X767

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