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Crystal structure of zika NS2B-NS3 protease with compound 1C

Analyse Crystal structure of zika NS2B-NS3 protease with compound 1C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JPW
Type: protein
Length: 788 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine protease subunit NS2B; NS3 protease; Ser-C0F-gly-lys-arg-lys
EC: 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
UniProt: Q32ZE1, A0A142IX72
Ligands: C0F
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48)	protein	38	0% helix, 47% strand	Q32ZE1
B, F, H	NS3 protease	protein	154	5% helix, 48% strand	A0A142IX72
D	NS3 protease	protein	159	4% helix, 45% strand	A0A142IX72
J, K, L	Ser-C0F-gly-lys-arg-lys	protein	5	0% helix, 40% strand	—

Ligands and binding sites

C0F · (4~{R})-2-[4-[(2~{S})-2,3-bis(azanyl)-3-oxidanylidene-propyl]pyridin-2-yl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid · ligand · 3 copies · chains C, D, J, E, F, K, G, H, L

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	372	0.62	0.77	54	empty
2	138	0.44	0.76	22	empty
3	140	0.44	0.76	24	empty
4	107	0.43	0.77	18	empty
5	94	0.38	0.76	21	empty

Interfaces

20 interfaces between chains.

E–F · 2034 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 2012 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1996 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1961 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 443 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

6JPW · Crystal structure of Zika NS2B-NS3 protease with compound 1C · 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 Q32ZE1
Every structure of UniProt A0A142IX72
Elsewhere: RCSB PDB 6JPW · PDBe 6JPW · UniProt Q32ZE1 · UniProt A0A142IX72

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