MolNFT v1 · #141896 · protein

Crystal structure of zika NS3 protease with phenylacetyl-lys-lys-arg- cooh inhibitor

5ZMQ · Serine protease subunit NS2B: “Crystal structure of zika NS3 protease with phenylacetyl-lys-lys-arg- cooh inhibitor”. X-ray diffraction, 1 ligand (PAC), 5 pockets (best druggability 0.58). MolNFT v1 #141896 on GenesisL1: 3D…

PDB: 5ZMQ
Type: protein
Length: 769 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine protease subunit NS2B; Serine protease NS3; Peptide pac-dly-dly-dar
EC: 3.4.21.91, 3.6.1.15, 3.6.4.13
UniProt: Q32ZE1, H8XX12
Ligands: PAC
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 8 distinct chains · 3% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	38	0% helix, 47% strand	Q32ZE1
B	Serine protease NS3	protein	153	5% helix, 50% strand	H8XX12
C	Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	37	0% helix, 43% strand	Q32ZE1
D	Serine protease NS3	protein	154	3% helix, 47% strand	H8XX12
F	Serine protease NS3	protein	150	5% helix, 51% strand	H8XX12
G	Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	39	0% helix, 46% strand	Q32ZE1
H	Serine protease NS3	protein	154	3% helix, 44% strand	H8XX12
I, K	Peptide pac-dly-dly-dar	protein	3	0% helix, 33% strand	—

Ligands and binding sites

PAC · 2-phenylacetic acid · ligand · 2 copies · chains D, E, I, H, K

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	348	0.58	0.76	41	empty
2	122	0.42	0.76	23	empty
3	92	0.38	0.76	16	empty
4	75	0.36	0.76	16	empty
5	85	0.36	0.75	18	empty

Interfaces

16 interfaces between chains.

A–B · 1990 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 1966 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 1929 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1854 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 400 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 d-amino, 2 covalent (D-amino acid, covalent ligand).

Compared structures

5ZMQ · Crystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-Arg-COOH inhibitor · 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 H8XX12
Elsewhere: RCSB PDB 5ZMQ · PDBe 5ZMQ · UniProt Q32ZE1 · UniProt H8XX12

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