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Crystal structure of the master-rep protein nuclease domain from the faba bean necrotic yellows virus

Analyse Crystal structure of the master-rep protein nuclease domain from the faba bean… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6H8O
Type: protein
Length: 190 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replication-associated protein
UniProt: A0A2D0XNJ4
Ligands: SO4
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Replication-associated protein	protein	95	15% helix, 48% strand	A0A2D0XNJ4

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B

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

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	561	0.66	0.77	64	SO4
2	50	0.37	0.80	17	empty
3	64	0.36	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 618 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6H8O · Crystal structure of the Master-Rep protein nuclease domain from the Faba Bean Necrotic… · 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 A0A2D0XNJ4
Elsewhere: RCSB PDB 6H8O · PDBe 6H8O · UniProt A0A2D0XNJ4

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