MolNFT v1 · #79134 · protein

Crystal structure of NS3/4A protease in complex with mk-5172

3SUD · NS3 protease, NS4A protein: “Crystal structure of NS3/4A protease in complex with mk-5172”. X-ray diffraction, 3 ligands (SUE, ZN, SO4), 10 pockets (best druggability 0.77). MolNFT v1 #79134 on GenesisL1: 3D structure, binding sites…

PDB: 3SUD
Type: protein
Length: 760 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NS3 protease, NS4A protein
UniProt: A8DG50
Ligands: SUE, ZN, SO4
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	NS3 protease, NS4A protein	protein	191	13% helix, 46% strand	A8DG50
C	NS3 protease, NS4A protein	protein	187	10% helix, 47% strand	A8DG50

Ligands and binding sites

SUE · (1aR,5S,8S,10R,22aR)-5-tert-butyl-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-14-methoxy-3,6-di oxo-1,1a,3,4,5,6,9,10,18,19,20,21,22,22a-tetradecahydro-8H-7,10-methanocyclopropa[18,19][1,10,3,6]dioxadiazacyclononadec ino[11,12-b]quinoxaline-8-carboxamide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · chains A, D

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	770	0.77	0.82	96	empty
2	371	0.58	0.75	38	SO4
3	233	0.54	0.77	37	empty
4	127	0.36	0.73	27	empty
5	75	0.35	0.76	16	empty

Interfaces

4 interfaces between chains.

A–C · 472 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 439 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 228 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 162 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3SUD · Crystal structure of NS3/4A protease in complex with MK-5172 · 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 A8DG50
Elsewhere: RCSB PDB 3SUD · PDBe 3SUD · UniProt A8DG50

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