Research workbench

The crystal structure of trypanosoma brucei RNase D : gmp complex

Analyse The crystal structure of trypanosoma brucei RNase D : gmp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7C4C
Type: protein
Length: 332 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cchc-type domain-containing protein
UniProt: Q38DE2
Ligands: 5GP, ZN, MN
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cchc-type domain-containing protein	protein	332	41% helix, 11% strand	Q38DE2

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A
ZN · Zinc ion · metal · 6 copies · chains A
MN · Manganese (II) ion · metal · 6 copies · chains A

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

Pockets

2 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	359	0.58	0.76	30	MN, 5GP
2	58	0.29	0.74	12	empty

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

7C4C · The crystal structure of Trypanosoma brucei RNase D : GMP complex · the same entry in another collection · chain A against A, 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 Q38DE2
Elsewhere: RCSB PDB 7C4C · PDBe 7C4C · UniProt Q38DE2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.