MolNFT v1 · #141947 · protein

Crystal structure of zika NS3 protease with 4-guanidinomethyl- phenylacetyl-arg-arg-arg-4-amidinobenzylamide

5ZOB · Serine protease subunit NS2B: “Crystal structure of zika NS3 protease with 4-guanidinomethyl- phenylacetyl-arg-arg-arg-4-amidinobenzylamide”. X-ray diffraction, 2 ligands (2UE, 00S), 7 pockets (best druggability 0.68). MolNFT v1…

PDB: 5ZOB
Type: protein
Length: 780 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine protease subunit NS2B; NS3 protease; 4-guanidinomethyl-phenylacetyl-arg-arg-arg-4…
EC: 3.4.21.91, 3.6.1.15, 3.6.4.13
UniProt: Q32ZE1, A0A142IX72
Ligands: 2UE, 00S
Pockets: 7 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 2% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	39	0% helix, 51% strand	Q32ZE1
B, D	NS3 protease	protein	156	3% helix, 45% strand	A0A142IX72
G, E	Serine protease subunit NS2B (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	38	0% helix, 42% strand	Q32ZE1
H, F	NS3 protease	protein	154	3% helix, 44% strand	A0A142IX72
I, J	4-guanidinomethyl-phenylacetyl-arg-arg-arg-4- amidinobenzylamide	protein	3	0% helix, 33% strand	—

Ligands and binding sites

2UE · 1-[4-(2-oxoethyl)benzyl]guanidine · ligand · 2 copies · chains B, C, I, A, D, J
00S · 4-(aminomethyl)benzenecarboximidamide · ligand · 2 copies · chains B, I, D, J

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

Pockets

7 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	569	0.68	0.78	61	2UE
2	127	0.40	0.74	24	empty
3	122	0.40	0.75	22	empty
4	107	0.40	0.76	23	empty
5	91	0.38	0.76	19	empty

Interfaces

16 interfaces between chains.

E–F · 2086 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2068 Å² buried · 34 hydrogen bonds · protein-protein
G–H · 2062 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2054 Å² buried · 33 hydrogen bonds · protein-protein
B–H · 434 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

5ZOB · Crystal structure of Zika NS3 protease with 4-guanidinomethyl-phenylacetyl-Arg-Arg-Arg-4-a… · 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 5ZOB · PDBe 5ZOB · UniProt Q32ZE1 · UniProt A0A142IX72

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