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Crystal structure of viral rdrp in complex with ATP

Analyse Crystal structure of viral rdrp in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HDH
Type: protein
Length: 1,226 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyprotein
EC: 2.7.7.48
UniProt: G3LHD9
Ligands: ATP, ZN
Pockets: 14 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Polyprotein (EC 2.7.7.48)	protein	613	47% helix, 12% strand	G3LHD9

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	821	0.87	0.90	104	empty
2	528	0.85	0.91	79	ATP
3	541	0.85	0.91	78	ATP
4	89	0.60	0.88	18	empty
5	242	0.56	0.78	34	empty

Interfaces

1 interface between chains.

A–B · 1288 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

4HDH · Crystal Structure of viral RdRp in complex with ATP · 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 G3LHD9
Elsewhere: RCSB PDB 4HDH · PDBe 4HDH · UniProt G3LHD9

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