Research workbench

Crystal structure of zika NS2B-NS3 protease with compound 5

Analyse Crystal structure of zika NS2B-NS3 protease with compound 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DOC
Type: protein
Length: 769 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Core protein; Genome polyprotein; 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
UniProt: A0A2R4LVW1, A0A142IX72, Q32ZE1, H8XX12
Ligands: HHC
Pockets: 7 · best druggability 0.67

Structure

x-ray diffraction · 8 distinct chains · 4% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	39	0% helix, 46% strand	A0A2R4LVW1
B	Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	153	5% helix, 48% strand	A0A142IX72
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	38	0% helix, 47% strand	Q32ZE1
D	Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	152	5% helix, 48% strand	A0A142IX72
E	Serine protease subunit NS2B	protein	39	0% helix, 44% strand	Q32ZE1
F	Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13)	protein	152	5% helix, 45% strand	A0A142IX72
H	Genome polyprotein	protein	153	5% helix, 48% strand	H8XX12
I	3-pyridin-4-yl-2,4-dihydro-INDENO[1,2-.C.]PYRAZOLE	protein	4	0% helix, 50% strand	—

Ligands and binding sites

HHC · ~{N}-[(2~{R})-2,3-bis(azanyl)-3-oxidanylidene-propyl]-2-[(4~{R})-4-methanoyl-4,5-dihydro-1,3-thiazol-2-yl]pyridine-4-carboxamide · ligand · chains A, B, I

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	483	0.67	0.78	58	empty
2	228	0.50	0.75	31	empty
3	132	0.46	0.78	22	empty
4	127	0.41	0.75	18	empty
5	129	0.41	0.75	22	empty

Interfaces

16 interfaces between chains.

G–H · 1967 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1952 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 1918 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 1883 Å² buried · 32 hydrogen bonds · protein-protein
F–H · 449 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7DOC · Crystal structure of Zika NS2B-NS3 protease with compound 5 · 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 A0A2R4LVW1
Every structure of UniProt A0A142IX72
Every structure of UniProt Q32ZE1
Every structure of UniProt H8XX12
Elsewhere: RCSB PDB 7DOC · PDBe 7DOC · UniProt A0A2R4LVW1 · UniProt A0A142IX72 · UniProt Q32ZE1 · UniProt H8XX12

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