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Crystal structure of eutv bound to RNA

Analyse Crystal structure of eutv bound to RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WW6
Type: protein + RNA
Length: 451 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Response regulator; Eutp P2
UniProt: A0A1Q1FU69
Ligands: BEF
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 5 distinct chains · 62% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Response regulator	protein	190	62% helix, 13% strand	A0A1Q1FU69
B	Response regulator	protein	192	63% helix, 13% strand	A0A1Q1FU69
E	Eutp P2	rna	17	—	—
F, D	Eutp P2	rna	17	—	—
C	Eutp P2	rna	18	—	—

Ligands and binding sites

BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B

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	143	0.54	0.81	20	empty
2	97	0.49	0.81	18	empty
3	158	0.49	0.78	20	empty
4	84	0.41	0.79	20	empty
5	90	0.35	0.74	15	empty

Interfaces

9 interfaces between chains.

A–B · 1991 Å² buried · 13 hydrogen bonds · protein-protein
E–D · 1805 Å² buried · 816 hydrogen bonds · nucleic-nucleic
F–C · 1764 Å² buried · 842 hydrogen bonds · nucleic-nucleic
B–C · 627 Å² buried · 20 hydrogen bonds · protein-nucleic
A–E · 616 Å² buried · 23 hydrogen bonds · protein-nucleic

Compared structures

6WW6 · Crystal structure of EutV bound to RNA · 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 A0A1Q1FU69
Elsewhere: RCSB PDB 6WW6 · PDBe 6WW6 · UniProt A0A1Q1FU69

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