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Crystal structure of zika NS2B-NS3 protease with compound 6

Analyse Crystal structure of zika NS2B-NS3 protease with compound 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6L4Z
Type: protein
Length: 761 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Genome polyprotein
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, H8XX12
Ligands: E5X
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 7 distinct chains · 2% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Genome polyprotein (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	Genome polyprotein	protein	155	3% helix, 48% strand	H8XX12
C	Genome polyprotein (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	37	0% helix, 46% strand	Q32ZE1
D	Genome polyprotein	protein	148	3% helix, 48% strand	H8XX12
F	Genome polyprotein	protein	152	3% helix, 48% strand	H8XX12
G	Genome polyprotein (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	40	0% helix, 45% strand	Q32ZE1
H	Genome polyprotein	protein	153	3% helix, 46% strand	H8XX12

Ligands and binding sites

E5X · 4-(hydroxymethyl)benzoic acid · ligand · chains H

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

Pockets

6 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	650	0.67	0.76	71	empty
2	151	0.44	0.75	26	empty
3	117	0.43	0.76	22	empty
4	100	0.41	0.77	17	empty
5	100	0.40	0.77	17	empty

Interfaces

12 interfaces between chains.

C–D · 1953 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1934 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1933 Å² buried · 34 hydrogen bonds · protein-protein
E–F · 1911 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 384 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6L4Z · Crystal structure of Zika NS2B-NS3 protease with compound 6 · 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 6L4Z · PDBe 6L4Z · UniProt Q32ZE1 · UniProt H8XX12

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