MolNFT v1 · #147481 · protein

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

6EEE · M17 leucyl-aminopeptidase: “X-ray crystal structure of pf-M17 in complex with inhibitor (6K) and regulatory zinc ion”. X-ray diffraction, 4 ligands (J4V, ZN, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #147481 on GenesisL1…

PDB: 6EEE
Type: protein
Length: 6,162 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: M17 leucyl-aminopeptidase
UniProt: A0A0L7KHE6
Ligands: J4V, ZN, SO4, CO3
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 9 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	M17 leucyl-aminopeptidase	protein	514	36% helix, 21% strand	A0A0L7KHE6
B	M17 leucyl-aminopeptidase	protein	511	35% helix, 22% strand	A0A0L7KHE6
C, I	M17 leucyl-aminopeptidase	protein	518	35% helix, 22% strand	A0A0L7KHE6
D, J	M17 leucyl-aminopeptidase	protein	516	35% helix, 22% strand	A0A0L7KHE6
E, K	M17 leucyl-aminopeptidase	protein	510	34% helix, 22% strand	A0A0L7KHE6
F	M17 leucyl-aminopeptidase	protein	509	36% helix, 22% strand	A0A0L7KHE6
G	M17 leucyl-aminopeptidase	protein	517	35% helix, 21% strand	A0A0L7KHE6
H	M17 leucyl-aminopeptidase	protein	513	36% helix, 22% strand	A0A0L7KHE6
L	M17 leucyl-aminopeptidase	protein	510	35% helix, 22% strand	A0A0L7KHE6

Ligands and binding sites

J4V · (1R,2r,3S,5R,7R)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]tricyclo[3.3.1.1~3,7~]decane-2-carboxamide · 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 · 31 copies · chains A, D, B, C, F, E, G, H, I, J, K, L
CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
1PE · Pentaethylene glycol · additive · 23 copies · chains A, B, C, D, F, G, H, I, J, K, L
EDO · 1,2-ethanediol · additive · 14 copies · chains E, F, G, I, H, J, K, L
DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B, G, H, K
2PE · Nonaethylene glycol · additive · chains H

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	993	0.79	0.81	106	J4V, CO3, SO4, DMS
2	1093	0.79	0.80	120	SO4, J4V, CO3
3	953	0.79	0.81	104	J4V, CO3, SO4
4	955	0.79	0.80	102	EDO, J4V
5	744	0.77	0.81	78	J4V, CO3, DMS

Interfaces

26 interfaces between chains.

H–I · 1519 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1502 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 1495 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1494 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1482 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

6EEE · X-ray crystal structure of Pf-M17 in complex with inhibitor (6k) and regulatory zinc ion · the same entry in another collection · chain I against I, 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 A0A0L7KHE6
Elsewhere: RCSB PDB 6EEE · PDBe 6EEE · UniProt A0A0L7KHE6

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