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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

3EBH

Structure of the M1 Alanylaminopeptidase from malaria complexed with bestatin

Functional Information from GO Data
ChainGOidnamespacecontents
A0006508biological_processproteolysis
A0008237molecular_functionmetallopeptidase activity
A0008270molecular_functionzinc ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 1
ChainResidue
AHIS496
AHIS500
AGLU519
ABES1085
site_idAC2
Number of Residues15
DetailsBINDING SITE FOR RESIDUE BES A1085
ChainResidue
AALA461
AGLU463
AHIS496
AGLU497
AHIS500
ALYS518
AGLU519
ATYR575
ATYR580
AHOH1604
AZN1
AGOL6
AGLU319
AVAL459
AGLY460
site_idAC3
Number of Residues10
DetailsBINDING SITE FOR RESIDUE GOL A1086
ChainResidue
AHOH19
ALYS479
ATYR880
AHIS886
AVAL887
AASP888
AGLN891
AARG895
ATYR925
AHOH1500
site_idAC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL A 2
ChainResidue
ATYR765
ACYS768
ATHR769
ATYR772
ATYR823
ASER826
APRO828
AHOH1489
AHOH1668
site_idAC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL A 3
ChainResidue
AHOH105
AHIS653
ALYS676
ATYR741
AASN835
APHE836
AHOH1661
site_idAC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE GOL A 4
ChainResidue
AHOH62
AVAL459
AGLY460
AASN471
AASN473
ASER474
AARG489
AASN994
AARG997
AHOH1604
site_idAC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL A 5
ChainResidue
AILE483
ATHR931
ASER934
ATHR966
AHOH1116
AHOH1153
AHOH1363
AHOH1584
site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL A 6
ChainResidue
ATYR575
ATYR580
ABES1085
AHOH1198
AHOH1648
site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 7
ChainResidue
AHOH26
AGLY250
AHOH1099
AHOH1212
AHOH1520
AHOH1521
site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 8
ChainResidue
AHOH1176
AHOH1523
AHOH1524
AHOH1525
AHOH1526
AHOH1527
site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 9
ChainResidue
AGLU957
AHOH1541
AHOH1542
AHOH1543
AHOH1544
site_idBC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 10
ChainResidue
AHOH100
AHOH103
AHOH1461
AHOH1566
AHOH1567
Functional Information from PROSITE/UniProt
site_idPS00142
Number of Residues10
DetailsZINC_PROTEASE Neutral zinc metallopeptidases, zinc-binding region signature. VVGHEYFHQY
ChainResidueDetails
AVAL493-TYR502
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P15144","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues3
DetailsBinding 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"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues1
DetailsBinding 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"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues3
DetailsBinding 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"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues1
DetailsSite: {"description":"Important for substrate specificity","evidences":[{"source":"PubMed","id":"23897806","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues1
DetailsSite: {"description":"Transition state stabilizer","evidences":[{"source":"UniProtKB","id":"P15144","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues1
DetailsSite: {"description":"Cleavage","evidences":[{"source":"PubMed","id":"21659511","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idCSA1
Number of Residues3
DetailsAnnotated By Reference To The Literature 1h19
ChainResidueDetails
ATYR580
AGLU463
AGLU497

243911

PDB entries from 2025-10-29

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