MolNFT v1 · #112829 · protein

X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based inhibitor 10B

4ZX9 · Probable M17 family aminopeptidase: “X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based inhibitor 10B”. X-ray diffraction, 4 ligands (4TK, ZN, CO3), 20 pockets (best druggability 0.77). MolNFT v1 #112829 on…

PDB: 4ZX9
Type: protein
Length: 6,170 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable M17 family aminopeptidase
EC: 3.4.11.1
UniProt: A0A024V0B1
Ligands: 4TK, ZN, CO3, SO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 11 distinct chains · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	519	35% helix, 22% strand	A0A024V0B1
B	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	516	34% helix, 22% strand	A0A024V0B1
C	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	517	34% helix, 22% strand	A0A024V0B1
D	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	513	35% helix, 22% strand	A0A024V0B1
E	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	509	35% helix, 22% strand	A0A024V0B1
F	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	511	34% helix, 22% strand	A0A024V0B1
H	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	517	33% helix, 22% strand	A0A024V0B1
I	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	518	34% helix, 22% strand	A0A024V0B1
J	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	512	33% helix, 22% strand	A0A024V0B1
K	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	508	35% helix, 23% strand	A0A024V0B1
L	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	511	35% helix, 22% strand	A0A024V0B1

Ligands and binding sites

4TK · N-[(1R)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]-2,2-dimethylpropanamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, 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
SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D, E, F, G, J, H, I, K, L
1PE · Pentaethylene glycol · additive · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
GOL · Glycerol · additive · 5 copies · chains A, D, B, G, I, J
DMS · Dimethyl sulfoxide · additive · 5 copies · chains C, A, D, G, 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	879	0.77	0.80	85	SO4
2	1076	0.77	0.79	107	4TK, CO3
3	732	0.76	0.80	78	empty
4	1020	0.75	0.78	113	empty
5	1191	0.74	0.77	129	empty

Interfaces

26 interfaces between chains.

H–I · 1503 Å² buried · 21 hydrogen bonds · protein-protein
G–I · 1500 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1490 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1490 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1489 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

4ZX9 · X-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10b · the same entry in another collection · chain J against J, 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 A0A024V0B1
Elsewhere: RCSB PDB 4ZX9 · PDBe 4ZX9 · UniProt A0A024V0B1

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