5Y1S

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(3,4-dimethylbenzyl)ureido)-N-hydroxy-4-methylpentanamide

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0006508	biological_process	proteolysis
A	0008237	molecular_function	metallopeptidase activity
A	0008270	molecular_function	zinc ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN A 1101

Chain	Residue
A	HIS496
A	HIS500
A	GLU519
A	E8F1105
A	E8R1106

---

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 1102

Chain	Residue
A	HOH1693
A	HOH1730
A	GLY250
A	HOH1302
A	HOH1403
A	HOH1677

---

site_id	AC3
Number of Residues	6
Details	binding site for residue MG A 1103

Chain	Residue
A	GLU526
A	HOH1458
A	HOH1459
A	HOH1656
A	HOH1673
A	HOH1744

---

site_id	AC4
Number of Residues	6
Details	binding site for residue MG A 1104

Chain	Residue
A	HOH1354
A	HOH1567
A	HOH1575
A	HOH1727
A	HOH1762
A	HOH1771

---

site_id	AC5
Number of Residues	20
Details	binding site for residue E8R A 1106

Chain	Residue
A	GLU319
A	VAL459
A	GLY460
A	ALA461
A	MET462
A	GLU463
A	ARG489
A	HIS496
A	GLU497
A	HIS500
A	GLU519
A	TYR580
A	ARG997
A	GLN1038
A	ZN1101
A	E8F1105
A	GOL1109
A	GOL1110
A	HOH1214
A	HOH1483

---

site_id	AC6
Number of Residues	9
Details	binding site for residue GOL A 1107

Chain	Residue
A	MET533
A	THR534
A	LYS535
A	HIS886
A	VAL887
A	ASP888
A	PHE889
A	ASP890
A	HOH1212

---

site_id	AC7
Number of Residues	6
Details	binding site for residue GOL A 1108

Chain	Residue
A	TYR853
A	SER903
A	LEU904
A	LYS907
A	HOH1209
A	HOH1679

---

site_id	AC8
Number of Residues	8
Details	binding site for residue GOL A 1109

Chain	Residue
A	TYR575
A	THR576
A	THR577
A	TYR580
A	E8F1105
A	E8R1106
A	GOL1110
A	HOH1231

---

site_id	AC9
Number of Residues	20
Details	binding site for residues E8F A 1105 and GOL A 1110

Chain	Residue
A	GLU319
A	VAL459
A	GLY460
A	ALA461
A	GLU463
A	ARG489
A	VAL493
A	HIS496
A	GLU497
A	HIS500
A	GLU519
A	GLU572
A	TYR575
A	TYR580
A	MET1034
A	ZN1101
A	E8R1106
A	GOL1109
A	HOH1214
A	HOH1656

---

site_id	AD1
Number of Residues	20
Details	binding site for residues E8F A 1105 and GOL A 1110

Chain	Residue
A	TYR580
A	MET1034
A	ZN1101
A	E8R1106
A	GOL1109
A	HOH1214
A	HOH1656
A	GLU319
A	VAL459
A	GLY460
A	ALA461
A	GLU463
A	ARG489
A	VAL493
A	HIS496
A	GLU497
A	HIS500
A	GLU519
A	GLU572
A	TYR575

---

site_id	AD2
Number of Residues	20
Details	binding site for residues E8F A 1105 and GOL A 1110

Chain	Residue
A	GLU319
A	VAL459
A	GLY460
A	ALA461
A	GLU463
A	ARG489
A	VAL493
A	HIS496
A	GLU497
A	HIS500
A	GLU519
A	GLU572
A	TYR575
A	TYR580
A	MET1034
A	ZN1101
A	E8R1106
A	GOL1109
A	HOH1214
A	HOH1656

---

site_id	AD3
Number of Residues	20
Details	binding site for residues E8F A 1105 and GOL A 1110

Chain	Residue
A	GLU319
A	VAL459
A	GLY460
A	ALA461
A	GLU463
A	ARG489
A	VAL493
A	HIS496
A	GLU497
A	HIS500
A	GLU519
A	GLU572
A	TYR575
A	TYR580
A	MET1034
A	ZN1101
A	E8R1106
A	GOL1109
A	HOH1214
A	HOH1656

---

site_id	AD4
Number of Residues	20
Details	binding site for residues E8F A 1105 and GOL A 1110

Chain	Residue
A	GLU319
A	VAL459
A	GLY460
A	ALA461
A	GLU463
A	ARG489
A	VAL493
A	HIS496
A	GLU497
A	HIS500
A	GLU519
A	GLU572
A	TYR575
A	TYR580
A	MET1034
A	ZN1101
A	E8R1106
A	GOL1109
A	HOH1214
A	HOH1656

---

site_id	AD5
Number of Residues	20
Details	binding site for residues E8F A 1105 and GOL A 1110

Chain	Residue
A	GLU319
A	VAL459
A	GLY460
A	ALA461
A	GLU463
A	ARG489
A	VAL493
A	HIS496
A	GLU497
A	HIS500
A	GLU519
A	GLU572
A	TYR575
A	TYR580
A	MET1034
A	ZN1101
A	E8R1106
A	GOL1109
A	HOH1214
A	HOH1656

---

site_id	AD6
Number of Residues	20
Details	binding site for residues E8F A 1105 and GOL A 1110

Chain	Residue
A	GLU319
A	VAL459
A	GLY460
A	ALA461
A	GLU463
A	ARG489
A	VAL493
A	HIS496
A	GLU497
A	HIS500
A	GLU519
A	GLU572
A	TYR575
A	TYR580
A	MET1034
A	ZN1101
A	E8R1106
A	GOL1109
A	HOH1214
A	HOH1656

---

Functional Information from PROSITE/UniProt

site_id	PS00142
Number of Residues	10
Details	ZINC_PROTEASE Neutral zinc metallopeptidases, zinc-binding region signature. VVGHEYFHNY

Chain	Residue	Details
A	VAL493-TYR502

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P15144","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19196988","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"21366301","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"3EBH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EBI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3Q43","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19196988","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"21366301","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"3EBH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3Q43","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19196988","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21366301","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21844374","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23713488","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23897806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25299353","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25645579","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26406322","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26807544","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30537832","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32182520","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2017","submissionDatabase":"PDB data bank","title":"Crystal structure of Plasmodium falciparum aminopeptidase N in complex with actinonin.","authors":["Marapaka A.K.","Addlagatta A."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2022","firstPage":"2550","lastPage":"2554","volume":"33","journal":"Chin. Chem. Lett.","title":"Development of peptidomimetic hydroxamates as PfA-M1 and PfA-M17 dual inhibitors: Biological evaluation and structural characterization by cocrystallization.","authors":["Marapaka A.K.","Sankoju P.","Zhang G.","Ding Y.","Ma C.","Pillalamarri V.","Sudhakar P.","Reddi B.","Sijwali P.S.","Zhang Y.","Addlagatta A."],"citationCrossReferences":[{"database":"DOI","id":"10.1016/j.cclet.2021.09.102"}]}},{"source":"PDB","id":"3T8V","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"5Y1Q","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"3EBG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EBH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3EBI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3Q43","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3Q44","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4J3B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4K5L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4K5M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4K5N","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4K5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4K5P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4R5T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4R5V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4R5X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4X2U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZQT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZW3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZW5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZW6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZW7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZW8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZX3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZX4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZX5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZX6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5XM7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y19","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y1H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y1K","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y1R","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y1S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y1T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y1V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y1W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y1X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5Y3I","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6EA1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6EA2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6EAA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6EAB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6EE3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6EE4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6EE6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6EED","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6SBQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6SBR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Site: {"description":"Important for substrate specificity","evidences":[{"source":"PubMed","id":"23897806","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Site: {"description":"Transition state stabilizer","evidences":[{"source":"UniProtKB","id":"P15144","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Site: {"description":"Cleavage","evidences":[{"source":"PubMed","id":"21659511","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---