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

Analyse X-ray crystal structure of pfa-M17 in complex with hydroxamic acid- based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZY1
Type: protein
Length: 6,169 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: 4U5, ZN, SO4, CO3
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 11 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	518	34% helix, 21% 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	516	34% helix, 22% strand	A0A024V0B1
D, J	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	514	36% helix, 22% strand	A0A024V0B1
E	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	508	35% helix, 22% strand	A0A024V0B1
F	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	511	35% helix, 22% strand	A0A024V0B1
G	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	519	34% helix, 21% 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	517	35% helix, 22% strand	A0A024V0B1
K	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	509	34% helix, 22% strand	A0A024V0B1
L	Probable M17 family aminopeptidase (EC 3.4.11.1)	protein	510	35% helix, 21% strand	A0A024V0B1

Ligands and binding sites

4U5 · N-{(1R)-2-(hydroxyamino)-1-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-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
SO4 · Sulfate ion · ion · 24 copies · chains A, D, B, C, E, F, G, J, H, I, 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 · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
GOL · Glycerol · additive · chains G, J

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	765	0.77	0.81	101	4U5
2	1117	0.75	0.78	106	4U5, CO3, SO4
3	904	0.75	0.78	104	empty
4	810	0.73	0.78	87	4U5, ZN, CO3
5	844	0.73	0.77	71	4U5, CO3, SO4

Interfaces

26 interfaces between chains.

B–C · 1520 Å² buried · 23 hydrogen bonds · protein-protein
H–I · 1502 Å² buried · 22 hydrogen bonds · protein-protein
G–I · 1485 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1484 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1475 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

4ZY1 · X-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10r · 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 A0A024V0B1
Elsewhere: RCSB PDB 4ZY1 · PDBe 4ZY1 · UniProt A0A024V0B1

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