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The crystal structure of trypanosoma brucei RNase D : ump complex

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

PDB: 7C4B
Type: protein
Length: 297 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cchc-type domain-containing protein
UniProt: Q38DE2
Ligands: U, ZN, MN
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cchc-type domain-containing protein	protein	297	44% helix, 12% strand	Q38DE2

Ligands and binding sites

U · Uridine-5'-monophosphate · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
MN · Manganese (II) ion · metal · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	417	0.57	0.74	37	MN

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

7C4B · The crystal structure of Trypanosoma brucei RNase D : UMP 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 7C4B · PDBe 7C4B · UniProt Q38DE2

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