MolNFT v1 · #120199 · protein

Crystal structures of EV71 3C protease in complex with nk-1.8K

5GSO · 3C protein: “Crystal structures of EV71 3C protease in complex with nk-1.8K”. X-ray diffraction, 1 ligand (5GI), 11 pockets (best druggability 0.55). MolNFT v1 #120199 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GSO
Type: protein
Length: 903 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C protein
UniProt: E7E815
Ligands: 5GI
Pockets: 11 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E	3C protein	protein	181	13% helix, 53% strand	E7E815
D	3C protein	protein	179	12% helix, 56% strand	E7E815

Ligands and binding sites

5GI · ~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]propan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.55	0.84	26	empty
2	237	0.52	0.76	25	empty
3	219	0.47	0.74	36	empty
4	223	0.46	0.73	30	empty
5	140	0.42	0.75	32	5GI

Interfaces

6 interfaces between chains.

C–D · 618 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 426 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 426 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 201 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 49 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

5GSO · Crystal Structures of EV71 3C Protease in complex with NK-1.8k · 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 E7E815
Elsewhere: RCSB PDB 5GSO · PDBe 5GSO · UniProt E7E815

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