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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE IN COMPLEX WITH COMPOUND 11D
 
Authors :  J. M. Rondeau, E. Bourgier
Date :  30 Jul 13  (Deposition) - 28 Aug 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Structure-Based Drug Design, Aspartyl Protease, Membrane, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Rueeger, R. Lueoend, R. Machauer, S. J. Veenstra, L. H. Jacobson, M. Staufenbiel, S. Desrayaud, J. M. Rondeau, H. Mobitz, U. Neumann
Discovery Of Cyclic Sulfoxide Hydroxyethylamines As Potent And Selective Beta-Site App-Cleaving Enzyme 1 (Bace1) Inhibitors: Structure Based Design And In Vivo Reduction Of Amyloid Beta-Peptides.
Bioorg. Med. Chem. Lett. V. 23 5300 2013
PubMed-ID: 23981898  |  Reference-DOI: 10.1016/J.BMCL.2013.07.071

(-) Compounds

Molecule 1 - BETA-SECRETASE 1
    Chains: A, B, C
    EC Number: 3.4.23.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 48-447
    Gene: BACE, BACE1, KIAA1149
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ASPARTYL PROTEASE 2, ASP2, ASP 2, BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME 1, MEMAPSIN-2, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
11YT3Ligand/Ion(1R,3S,4S,5R)-3-(4-AMINO-3-FLUORO-5-{[(2R)-1,1,1-TRIFLUORO-3-METHOXYPROPAN-2-YL]OXY}BENZYL)-5-[(3-TERT-BUTYLBENZYL)AMINO]TETRAHYDRO-2H-THIOPYRAN-4-OL 1-OXIDE
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11YT1Ligand/Ion(1R,3S,4S,5R)-3-(4-AMINO-3-FLUORO-5-{[(2R)-1,1,1-TRIFLUORO-3-METHOXYPROPAN-2-YL]OXY}BENZYL)-5-[(3-TERT-BUTYLBENZYL)AMINO]TETRAHYDRO-2H-THIOPYRAN-4-OL 1-OXIDE
2GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
11YT1Ligand/Ion(1R,3S,4S,5R)-3-(4-AMINO-3-FLUORO-5-{[(2R)-1,1,1-TRIFLUORO-3-METHOXYPROPAN-2-YL]OXY}BENZYL)-5-[(3-TERT-BUTYLBENZYL)AMINO]TETRAHYDRO-2H-THIOPYRAN-4-OL 1-OXIDE
2GOL1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
11YT1Ligand/Ion(1R,3S,4S,5R)-3-(4-AMINO-3-FLUORO-5-{[(2R)-1,1,1-TRIFLUORO-3-METHOXYPROPAN-2-YL]OXY}BENZYL)-5-[(3-TERT-BUTYLBENZYL)AMINO]TETRAHYDRO-2H-THIOPYRAN-4-OL 1-OXIDE
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , GLN A:12 , GLY A:13 , LEU A:30 , ASP A:32 , GLY A:34 , SER A:35 , VAL A:69 , PRO A:70 , TYR A:71 , THR A:72 , GLN A:73 , GLY A:74 , PHE A:108 , ASP A:228 , GLY A:230 , THR A:231 , THR A:232 , HOH A:658 , HOH A:686 , HOH A:749BINDING SITE FOR RESIDUE 1YT A 501
2AC2SOFTWAREARG B:205 , VAL B:375 , THR B:376BINDING SITE FOR RESIDUE GOL B 501
3AC3SOFTWAREGLN B:12 , GLY B:13 , LEU B:30 , ASP B:32 , GLY B:34 , SER B:35 , VAL B:69 , PRO B:70 , TYR B:71 , THR B:72 , GLN B:73 , GLY B:74 , PHE B:108 , TYR B:198 , ASP B:228 , GLY B:230 , THR B:231 , THR B:232 , HOH B:717 , HOH B:727 , HOH B:785BINDING SITE FOR RESIDUE 1YT B 502
4AC4SOFTWAREGLY C:11 , GLN C:12 , GLY C:13 , LEU C:30 , ASP C:32 , GLY C:34 , SER C:35 , VAL C:69 , PRO C:70 , TYR C:71 , THR C:72 , GLN C:73 , PHE C:108 , ILE C:110 , TRP C:115 , ILE C:126 , ASP C:228 , GLY C:230 , THR C:231 , THR C:232 , HOH C:616 , HOH C:621 , HOH C:672 , HOH C:813BINDING SITE FOR RESIDUE 1YT C 501

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:155 -A:359
2A:217 -A:382
3A:269 -A:319
4B:155 -B:359
5B:217 -B:382
6B:269 -B:319
7C:155 -C:359
8C:217 -C:382
9C:269 -C:319

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:22 -Pro A:23
2Arg A:128 -Pro A:129
3Tyr A:222 -Asp A:223
4Gly A:372 -Pro A:373
5Ser B:22 -Pro B:23
6Arg B:128 -Pro B:129
7Tyr B:222 -Asp B:223
8Gly B:372 -Pro B:373
9Ser C:22 -Pro C:23
10Arg C:128 -Pro C:129
11Tyr C:222 -Asp C:223
12Gly C:372 -Pro C:373

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LXK)

(-) 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4lxka_ A: beta-secretase (memapsin)                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eee.....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee.......eeeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeee...eeeeeee...hhh.eeeeeeeee..........eeeeee..ee...hhhhhhh..eee......eeeehhhhhhhhhhhhhhh.....hhhhhh....eee.....hhhhh..eeeeee.....eeeeeeehhhhheeee........eeeee.eeee...eeehhhhhh.eeeeeehhh.eeeeeee...........eeeeeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lxk A 46P SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGSVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                            ||||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      
                            ||||                                                                                                                                                        156|                                                                                                                                                                                                                        
                          46P|||                                                                                                                                                         169                                                                                                                                                                                                                        
                           47P||                                                                                                                                                                                                                                                                                                                                                                                    
                            48P|                                                                                                                                                                                                                                                                                                                                                                                    
                               1                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4lxkb_ B: beta-secretase (memapsin)                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..eeee....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee.......eeeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeee....eeeeeeee...hhh.eeeeeeeee..........eeeeee..ee...hhhhhhh..eee......eeeehhhhhhhhhhhhhhh.....hhhhhh....eeee....hhhhh..eeeeee.....eeeeeeehhhhheeee.......eeeeee.eeee...eeehhhhhh.eeeeeehhh.eeeeeee...........eeeeeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lxk B 46P SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                            ||||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157|      177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377        
                          46P|||                                                                                                                                                         157|                                                                                                                                                                                                                         
                           47P||                                                                                                                                                          168                                                                                                                                                                                                                         
                            48P|                                                                                                                                                                                                                                                                                                                                                                                      
                               1                                                                                                                                                                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4lxkc_ C: beta-secretase (memapsin)                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eee.....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee........eeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeee........eeeeeee...hhh.eeeeeeeee..........eeeeee..ee...hhhhhhh..eee......eeeehhhhhhhhhhhhhhh.....hhhhhh....eee.....hhhhh..eeeee.......eeeeeehhhhheeee........eeeee.eeee...eeehhhhhh.eeeeeehhh.eeeeeee...........eeeeee...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lxk C 46P SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                            ||||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  ||   174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384 
                          46P|||                                                                                                                                                            160|                                                                                                                                                                                                                         
                           47P||                                                                                                                                                             168                                                                                                                                                                                                                         
                            48P|                                                                                                                                                                                                                                                                                                                                                                                         
                               1
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)

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  4lxk
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  BACE1_HUMAN | P56817
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  3.4.23.46
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 Related Entries

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

UniProtKB/Swiss-Prot
        BACE1_HUMAN | P56817: 1fkn 1m4h 1py1 1sgz 1tqf 1ujj 1ujk 1w50 1w51 1xn2 1xn3 1xs7 1ym2 1ym4 2b8l 2b8v 2f3e 2f3f 2fdp 2g94 2hiz 2hm1 2iqg 2irz 2is0 2ntr 2oah 2of0 2ohk 2ohl 2ohm 2ohn 2ohp 2ohq 2ohr 2ohs 2oht 2ohu 2p4j 2p83 2p8h 2ph6 2ph8 2q11 2q15 2qk5 2qmd 2qmf 2qmg 2qp8 2qu2 2qu3 2qzk 2qzl 2va5 2va6 2va7 2vie 2vij 2viy 2viz 2vj6 2vj7 2vj9 2vkm 2vnm 2vnn 2wez 2wf0 2wf1 2wf2 2wf3 2wf4 2wjo 2xfi 2xfj 2xfk 2zdz 2ze1 2zhr 2zhs 2zht 2zhu 2zhv 2zjh 2zji 2zjj 2zjk 2zjl 2zjm 2zjn 3bra 3buf 3bug 3buh 3cib 3cic 3cid 3ckp 3ckr 3dm6 3duy 3dv1 3dv5 3exo 3fkt 3h0b 3hvg 3hw1 3i25 3igb 3in3 3in4 3ind 3ine 3inf 3inh 3ivh 3ivi 3ixj 3ixk 3k5c 3k5d 3k5f 3k5g 3kmx 3kmy 3kn0 3kyr 3l38 3l3a 3l58 3l59 3l5b 3l5c 3l5d 3l5e 3l5f 3lhg 3lnk 3lpi 3lpj 3lpk 3msj 3msk 3msl 3n4l 3nsh 3ohf 3ohh 3ooz 3pi5 3qbh 3qi1 3r1g 3r2f 3rsv 3rsx 3rth 3rtm 3rtn 3ru1 3rvi 3s2o 3s7l 3s7m 3skf 3skg 3tpj 3tpl 3tpp 3tpr 3u6a 3udh 3udj 3udk 3udm 3udn 3udp 3udq 3udr 3udy 3ufl 3uqp 3uqr 3uqu 3uqw 3uqx 3veu 3vf3 3vg1 3vv6 3vv7 3vv8 3wb4 3wb5 3zmg 3zov 4acu 4acx 4azy 4b00 4b05 4b0q 4b1c 4b1d 4b1e 4b70 4b72 4b77 4b78 4bek 4bfd 4d83 4d85 4d88 4d89 4d8c 4dh6 4di2 4dju 4djv 4djw 4djx 4djy 4dpf 4dpi 4dus 4dv9 4dvf 4ewo 4exg 4fco 4fgx 4fm7 4fm8 4fri 4frj 4frk 4frs 4fs4 4fse 4fsl 4gid 4gmi 4h1e 4h3f 4h3g 4h3i 4h3j 4ha5 4hzt 4i0d 4i0e 4i0f 4i0g 4i0h 4i0i 4i0j 4i0z 4i10 4i11 4i12 4i1c 4ivs 4ivt 4j0p 4j0t 4j0v 4j0y 4j0z 4j17 4j1c 4j1e 4j1f 4j1h 4j1i 4j1k 4joo 4jp9 4jpc 4jpe 4k8s 4k9h 4ke0 4ke1 4l7g 4l7h 4l7j 4lc7 4lxa 4lxm 4n00 4pzw 4pzx 4r5n 4r8y 4r91 4r92 4r93 4r95 4rcd 4rce 4rcf 4rrn 4rro 4rrs 4trw 4try 4trz 4wtu 4wy1 4wy6 4x2l 4x7i 4xkx 4xxs 4ybi 4zpe 4zpf 4zpg 4zsm 4zsp 4zsq 4zsr 5clm 5dqc 5enk 5enm 5ezx 5ezz 5f00 5f01 5hd0 5hdu 5hdv 5hdx 5hdz 5he4 5he5 5he7 5htz 5hu0 5hu1 5i3v 5i3w 5i3x 5i3y 5ie1 5kqf 5kr8 5t1u 5t1w 5tol 5uyu 5v0n

(-) Related Entries Specified in the PDB File

4lxa BACE1 COMPLEX WITH COMPOUND 11A
4lxm BACE1 IN COMPLEX WITH COMPOUND 12A