7M1V: Core protein

Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the super-open conformation. Determined by X-ray diffraction at 1.6 Å resolution. Released 21 Apr 2021.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Zika virus
Chains: 2
Atoms: 2,936
Mol. weight: 47.21 kDa
Ligands: YO1
Released: 21 Apr 2021

Explore 7M1V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M1V contains 5 α-helices and 37 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	50-57	8	1
β-strand	66-67	2	2
β-strand	1021-1029	9	1
β-strand	1032-1042	11	1
β-strand	1045-1048	4	1
α-helix	1050-1053	4
β-strand	1058-1060	3	1
β-strand	1063-1065	3	1
β-strand	1067-1071	5	1
β-strand	1076-1079	4	1
β-strand	1089	1	3
β-strand	1095-1099	5	2
β-strand	1107-1111	5	2
β-strand	1114-1118	5	2
β-strand	1121-1125	5	2
α-helix	1132-1134	3
α-helix	1137	1
β-strand	1138-1140	3	2
β-strand	1146-1149	4	2
β-strand	1153-1154	2	2
β-strand	1156	1	3

Chain B: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	50-57	8	4
β-strand	66-67	2	5
β-strand	1021-1029	9	4
β-strand	1032-1042	11	4
β-strand	1045-1048	4	4
α-helix	1050-1053	4
β-strand	1058	1	6
β-strand	1059	1	4
β-strand	1065	1	6
β-strand	1067-1071	5	4
β-strand	1076-1079	4	4
β-strand	1089	1	7
β-strand	1095-1099	5	5
β-strand	1107-1111	5	5
β-strand	1114-1117	4	8
β-strand	1122-1125	4	8
β-strand	1138-1140	3	5
β-strand	1146-1149	4	5
β-strand	1154-1155	2	8
β-strand	1156	1	7
α-helix	1157	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Core protein	A, B	protein	221	Zika virus	A0A024B7W1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7M1V_1 Core protein (chains A, B)
GPLGSSVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEDDGPPMAGGGGSGG
GGSGALWDVPAPKEVKKGETTDGVYRVMTRRTSGSTQVGVGVMQEGVFHTMWHVTKGSAL
RSGEGRLDPYWGDVKQDLVSYSGPWKLDACWDGHSEVQLLAVPPGERARNIQTLPGIFKT
KDGDIGAVALDYPAGTSGSPILDKSGRVIGLYGNGVVICNG

Ligands and cofactors

ID	Name	Formula	Copies
YO1	4-(2-{2,4-diamino-5-[2-(4-{[(2E)-1,3-thiazolidin-2-ylidene]sulfamoyl}phenyl)hyd…	C24 H20 N10 O4 S4	1

Water and common crystallization additives (DMS, CL, EDO) are not listed.

Primary citation

To be provided. Aleshin, A.E., Shiryaev, S.A., Liddington, R.C. To be published.

Other PDB entries of the same protein (UniProt A0A024B7W1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KQR 1.33 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine
6LD1 1.4 Å, Zika NS5 polymerase domain
6LD2 1.4 Å, Zika NS5 polymerase domain
5KQS 1.5 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and…
6LD4 1.5 Å, Zika NS5 polymerase domain
6S0J 1.5 Å, Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)-
5ULP 1.55 Å, Structure of the NS5 methyltransferase from Zika bound to MS2042
5Y6N 1.57 Å, Zika virus helicase in complex with ADP
5KVE 1.7 Å, Zika specific antibody, ZV-48, bound to ZIKA envelope DIII
6RWZ 1.7 Å, Structure of Zika virus NS3 helicase in complex with ADP-BeF3
5JMT 1.8 Å, Crystal structure of Zika virus NS3 helicase
5MRK 1.9 Å, Structural basis of Zika virus methyltransferase inhibition by sinefungin

Browse structure collections

About this viewer

MolViewer shows 7M1V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.