MolNFT v1 · #147469 · protein

X-ray crystal structure of pf-M17 in complex with inhibitor 6I and regulatory zinc ion

6EE2: “X-ray crystal structure of pf-M17 in complex with inhibitor 6I and regulatory zinc ion”. X-ray diffraction, 4 ligands (J1V, ZN, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #147469 on GenesisL1: 3D structure, binding sites…

PDB: 6EE2
Type: protein
Length: 6,189 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pf-M17
UniProt: W4I9J7
Ligands: J1V, ZN, SO4, CO3
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 10 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Pf-M17	protein	519	35% helix, 22% strand	W4I9J7
B	Pf-M17	protein	518	36% helix, 22% strand	W4I9J7
C, H	Pf-M17	protein	520	36% helix, 22% strand	W4I9J7
D	Pf-M17	protein	516	35% helix, 22% strand	W4I9J7
E	Pf-M17	protein	510	35% helix, 22% strand	W4I9J7
F	Pf-M17	protein	510	35% helix, 22% strand	W4I9J7
I	Pf-M17	protein	523	35% helix, 21% strand	W4I9J7
J	Pf-M17	protein	512	36% helix, 22% strand	W4I9J7
K	Pf-M17	protein	509	35% helix, 22% strand	W4I9J7
L	Pf-M17	protein	513	36% helix, 22% strand	W4I9J7

Ligands and binding sites

J1V · N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]cyclohexanecarboxamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
SO4 · Sulfate ion · ion · 23 copies · chains A, B, C, F, E, D, G, H, I, K, J, L
CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
1PE · Pentaethylene glycol · additive · 37 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, B, C, D, E, G, I, J, K, L
EDO · 1,2-ethanediol · additive · 2 copies · chains I

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.79	0.81	105	CO3, J1V
2	1003	0.79	0.81	104	CO3, J1V, SO4
3	1027	0.79	0.81	104	CO3, J1V, SO4
4	820	0.78	0.81	85	CO3, J1V
5	1006	0.76	0.79	98	empty

Interfaces

26 interfaces between chains.

A–B · 1510 Å² buried · 26 hydrogen bonds · protein-protein
G–I · 1503 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 1503 Å² buried · 26 hydrogen bonds · protein-protein
H–I · 1502 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1500 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

6EE2 · X-ray crystal structure of Pf-M17 in complex with inhibitor 6i and regulatory zinc ion · 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 W4I9J7
Elsewhere: RCSB PDB 6EE2 · PDBe 6EE2 · UniProt W4I9J7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.