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(-) Description

Title :  STRUCTURE OF CYSTEINE-FREE HUMAN INSULIN DEGRADING ENZYME IN COMPLEX WITH MACROCYCLIC INHIBITOR
 
Authors :  Z. H. Foda, M. A. Seeliger, A. Saghatelian, D. R. Liu
Date :  23 Jul 13  (Deposition) - 21 May 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B,M,N
Biol. Unit 1:  A,M  (1x)
Biol. Unit 2:  B,N  (1x)
Keywords :  Hydrolase, Metal-Binding, Metalloprotease, Protease, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Maianti, A. Mcfedries, Z. H. Foda, R. E. Kleiner, X. Q. Du, M. A. Leissring, W. J. Tang, M. J. Charron, M. A. Seeliger, A. Saghatelian, D. R. Liu
Anti-Diabetic Activity Of Insulin-Degrading Enzyme Inhibitors Mediated By Multiple Hormones.
Nature V. 511 94 2014
PubMed-ID: 24847884  |  Reference-DOI: 10.1038/NATURE13297

(-) Compounds

Molecule 1 - INSULIN-DEGRADING ENZYME
    Chains: A, B
    EC Number: 3.4.24.56
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX-H6
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 42-1019
    Gene: IDE
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ABETA-DEGRADING PROTEASE, INSULIN PROTEASE, INSULINASE, INSULYSIN
 
Molecule 2 - MACROCYCLIC INHIBITOR
    Chains: M, N
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABMN
Biological Unit 1 (1x): A M 
Biological Unit 2 (1x):  B N

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1DFF2Mod. Amino Acid4-BENZOYL-D-PHENYLALANINE
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3FUM2Mod. Amino AcidFUMARIC ACID
4LYN2Mod. Amino Acid2,6-DIAMINO-HEXANOIC ACID AMIDE
5ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1DFF1Mod. Amino Acid4-BENZOYL-D-PHENYLALANINE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3FUM1Mod. Amino AcidFUMARIC ACID
4LYN1Mod. Amino Acid2,6-DIAMINO-HEXANOIC ACID AMIDE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1DFF1Mod. Amino Acid4-BENZOYL-D-PHENYLALANINE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3FUM1Mod. Amino AcidFUMARIC ACID
4LYN1Mod. Amino Acid2,6-DIAMINO-HEXANOIC ACID AMIDE
5ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:108 , HIS A:112 , GLU A:189 , HOH A:1371BINDING SITE FOR RESIDUE ZN A 1101
2AC2SOFTWAREGLN A:800 , ARG A:839 , ALA A:840 , ASN A:841 , GLY A:842 , SER A:913 , ARG A:920 , HOH A:1400 , HOH A:1416BINDING SITE FOR RESIDUE EPE A 1102
3AC3SOFTWAREHIS B:108 , HIS B:112 , GLU B:189 , HOH B:1255BINDING SITE FOR RESIDUE ZN B 1101
4AC4SOFTWAREGLN B:800 , ALA B:840 , ASN B:841 , GLY B:842 , GLU B:910 , SER B:913 , ARG B:920 , HOH B:1268BINDING SITE FOR RESIDUE EPE B 1102
5AC5SOFTWAREALA A:198 , TRP A:199 , LEU A:201 , PHE A:202 , LEU A:204 , GLU A:205 , TYR A:302 , TYR A:314 , THR A:316 , VAL A:360 , GLN A:363 , LYS A:364 , ARG A:477BINDING SITE FOR CHAIN M OF MACROCYCLIC INHIBITOR
6AC6SOFTWAREALA B:198 , TRP B:199 , LEU B:201 , PHE B:202 , LEU B:204 , GLU B:205 , TYR B:314 , THR B:316 , VAL B:360 , GLN B:363 , LYS B:364 , ARG B:477 , HOH B:1366BINDING SITE FOR CHAIN N OF MACROCYCLIC INHIBITOR

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LTE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr B:625 -Gly B:626

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LTE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LTE)

(-) Exons   (0, 0)

(no "Exon" information available for 4LTE)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:954
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee............eeeeeee....eeeeee.....eeeeeeee..hhhhh.....hhhhhhhhhhhhh.......hhhhhhhhh...eeeeee....eeeeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhh.................hhhhh.eeeee.......eeeeeeee..hhhhh..hhhhhhhhhhh.....hhhhhhhhh.....eeeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhh..........hhhhhhhhhhhhhhhh.eeeee.hhhh....ee......eeeeee.hhhhhhhhhh.................................eeeee...eeeeeee.......eeeeeeeee.hhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.ee.hhhhh...........eeeeeeee......eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhh.......eeeeeeee................ee..hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4lte A   44 NPAIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDVHIGSLSDPPNIAGLSHFLQHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDRFAQFFLSPLFDESAKDREVNAVDSEHEKNVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVRQELLKFHSAYYSSNLMAVVVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSNPGHYLGHLIGHEGPGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIILHMFQYIQKLRAEGPQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILHYYPLEEVLTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRTEEWYGTQYKQEAIPDEVIKKWQNADLNGKFKLPTKNEFIPTNFEILPLEKEATPYPALIKDTAMSKLWFKQDDKFFLPKANLNFEFFSPFAYVDPLHSNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILLKKIIEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTEVAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIMQMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQQRNEVHNNSGIEIYYQTDMQSTSENMFLELFAQIISEPAFNTLRTKEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLITMEKSIEDMTEEAFQKHIQALAIRRLDKPKKLSAESAKYWGEIISQQYNFDRDNTEVAYLKTLTKEDIIKFYKEMLAVDAPRRHKVSVHVLAREMINLSQAPALPQPEVIQNMTEFKRGLPLFPLVKPH 1011
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963|      987       997      1007    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 963|                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  978                                 


Chain B from PDB  Type:PROTEIN  Length:954
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...........eeeeeee....eeeeee.....eeeeeeee..hhhhh.....hhhhhhhhhh..........hhhhhhhhhh..eeeeee....eeeeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhh.................hhhhh.eeeee.......eeeeeeee..hhhhh..hhhhhhhhhhh.....hhhhhhhhh.....eeeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhh..........hhhhhhhhhhhhhhhh.eeeee.hhhh....ee......eeeeee.hhhhhhhhhh.................................eeeee...eeeeeee.......eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.ee.hhhhh...........eeeeeeee......eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhh.......eeeeeeee................ee..hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4lte B   44 NPAIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDVHIGSLSDPPNIAGLSHFLQHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDRFAQFFLSPLFDESAKDREVNAVDSEHEKNVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVRQELLKFHSAYYSSNLMAVVVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSNPGHYLGHLIGHEGPGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIILHMFQYIQKLRAEGPQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILHYYPLEEVLTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRTEEWYGTQYKQEAIPDEVIKKWQNADLNGKFKLPTKNEFIPTNFEILPLEKEATPYPALIKDTAMSKLWFKQDDKFFLPKANLNFEFFSPFAYVDPLHSNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILLKKIIEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTEVAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIMQMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQQRNEVHNNSGIEIYYQTDMQSTSENMFLELFAQIISEPAFNTLRTKEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLITMEKSIEDMTEEAFQKHIQALAIRRLDKPKKLSAESAKYWGEIISQQYNFDRDNTEVAYLKTLTKEDIIKFYKEMLAVDAPRRHKVSVHVLAREMINLSQAPALPQPEVIQNMTEFKRGLPLFPLVKPH 1011
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963|      987       997      1007    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 963|                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  978                                 


Chain M from PDB  Type:PROTEIN  Length:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                4lte M    1 Fxkx    4
                             |||
                             2-DFF
                              3-LYN
                               4-FUM


Chain N from PDB  Type:PROTEIN  Length:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                4lte N    1 Fxkx    4
                             |||
                             |||
                             2-DFF
                              3-LYN
                               4-FUM
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4LTE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LTE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LTE)

(-) Gene Ontology  (53, 53)

Asymmetric Unit(hide GO term definitions)

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  4lte
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  IDE_HUMAN | P14735
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IDE_HUMAN | P14735: 2g47 2g48 2g49 2g54 2g56 2jbu 2jg4 2wby 2wc0 2wk3 2ypu 3cww 3e4a 3e4z 3e50 3h44 3hgz 3n56 3n57 3ofi 3qz2 4dtt 4dwk 4gs8 4gsc 4gsf 4ifh 4iof 4m1c 4nxo 4pes 4pf7 4pf9 4pfc 4q5z 4qia 4ral 4re9 5cjo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4LTE)