MolNFT v1 · #141778 · protein

Crystal structure of human enterovirus D68 rdrp in complex with NADPH

5ZIT: “Crystal structure of human enterovirus D68 rdrp in complex with NADPH”. X-ray diffraction, 1 ligand (NDP), 3 pockets (best druggability 0.67). MolNFT v1 #141778 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZIT
Type: protein
Length: 456 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rdrp
EC: 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
UniProt: I6TFG7
Ligands: NDP
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rdrp (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48)	protein	456	41% helix, 16% strand	I6TFG7

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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	654	0.67	0.76	61	NDP
2	198	0.42	0.72	25	empty
3	94	0.42	0.78	21	empty

Compared structures

5ZIT · Crystal structure of human Enterovirus D68 RdRp in complex with NADPH · 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 I6TFG7
Elsewhere: RCSB PDB 5ZIT · PDBe 5ZIT · UniProt I6TFG7

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