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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BUTYRYLCHOLINESTERASE IN COMPLEX WITH N-((1-BENZYLPIPERIDIN-3-YL)METHYL)-N-METHYLNAPHTHALENE-2-SULFONAMIDE
 
Authors :  N. Coquelle, B. Brus, J. P. Colletier
Date :  25 Sep 15  (Deposition) - 05 Oct 16  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human Butyrylcholinesterase, Ad, Alzheimer Disease, Sulfonamide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Kosak, B. Brus, D. Knez, R. Sink, S. Zakelj, J. Trontelj, A. Pislar, J. Slenc, M. Gobec, M. Zivin, L. Tratnjek, M. Perse, K. Saat, A. Podkowa B. Filipek, F. Nachon, X. Brazzolotto, A. Wieckowska, B. Malawska, J. Stojan, I. M. Rascan, J. Kos, N. Coquelle, J. P. Colletier, S. Gobec
Development Of An In-Vivo Active Reversible Butyrylcholinesterase Inhibitor.
Sci Rep V. 6 39495 2016
PubMed-ID: 28000737  |  Reference-DOI: 10.1038/SREP39495

(-) Compounds

Molecule 1 - CHOLINESTERASE
    Chains: A, B
    EC Number: 3.1.1.8
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Common: FRUIT FLY
    Expression System Taxid: 7227
    Fragment: UNP RSIDUES 28-557
    Gene: BCHE, CHE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ACYLCHOLINE ACYLHYDROLASE,BUTYRYLCHOLINE ESTERASE,CHOLINE ESTERASE II,PSEUDOCHOLINESTERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 46)

Asymmetric/Biological Unit (9, 46)
No.NameCountTypeFull Name
15HB2Ligand/IonN-{[(3R)-1-BENZYLPIPERIDIN-3-YL]METHYL}-N-METHYLNAPHTHALENE-2-SULFONAMIDE
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3EDO4Ligand/Ion1,2-ETHANEDIOL
4FUC4Ligand/IonALPHA-L-FUCOSE
5FUL1Ligand/IonBETA-L-FUCOSE
6GOL5Ligand/IonGLYCEROL
7NAG21Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
9UNX6Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:116 , GLY A:117 , GLN A:119 , THR A:120 , SER A:198 , SER A:287 , TRP A:430 , HIS A:438 , HOH A:703binding site for residue 5HB A 616
02AC2SOFTWARELEU A:18 , TRP A:98 , ASP A:129 , LYS A:131binding site for residue GOL A 617
03AC3SOFTWAREASN A:228 , TYR A:396 , PRO A:401 , TRP A:522 , THR A:523 , HOH A:760binding site for residue GOL A 618
04AC4SOFTWARETYR A:33 , SER A:48 , LEU A:49 , LEU A:173 , TRP A:177binding site for residue GOL A 619
05AC5SOFTWAREHIS A:77 , GLU A:443binding site for residue EDO A 620
06AC6SOFTWAREPHE B:278 , NAG B:604 , NAG B:605binding site for residue FUL B 606
07AC7SOFTWAREGLY B:116 , GLY B:117 , GLN B:119 , THR B:120 , SER B:198 , TRP B:231 , LEU B:286 , SER B:287 , PHE B:329 , TRP B:430 , MET B:437 , HIS B:438 , TYR B:440 , HOH B:711 , HOH B:812binding site for residue 5HB B 612
08AC8SOFTWARELEU B:18 , TYR B:61 , TRP B:98 , ASP B:129 , LYS B:131binding site for residue GOL B 613
09AC9SOFTWARETRP B:231 , LEU B:286 , SER B:287 , VAL B:288 , ASN B:397 , EDO B:616binding site for residue GOL B 614
10AD1SOFTWAREARG B:42 , LYS B:267 , PRO B:269binding site for residue EDO B 615
11AD2SOFTWAREPRO B:230 , TRP B:231 , VAL B:233 , THR B:234 , GLU B:238 , VAL B:288 , GOL B:614binding site for residue EDO B 616
12AD3SOFTWAREASN B:455binding site for residue EDO B 617
13AD4SOFTWAREHIS B:77 , MET B:81 , SER B:425 , LYS B:427 , LEU B:428 , PRO B:429 , GLU B:443binding site for residue PEG B 621
14AD5SOFTWAREASN A:17binding site for Mono-Saccharide NAG A 601 bound to ASN A 17
15AD6SOFTWAREILE A:55 , ASN A:57binding site for Poly-Saccharide residues NAG A 602 through FUC A 604 bound to ASN A 57
16AD7SOFTWAREASN A:106 , ASN A:188 , LYS A:190binding site for Poly-Saccharide residues NAG A 605 through NAG A 606 bound to ASN A 106
17AD8SOFTWAREASN A:241 , ASN A:245 , LYS A:248 , PHE A:278 , PRO A:281 , NAG B:609 , FUC B:610binding site for Poly-Saccharide residues NAG A 607 through FUC A 609 bound to ASN A 241
18AD9SOFTWARESER A:338 , ASN A:341 , HOH A:713 , HOH A:793 , HOH A:798binding site for Mono-Saccharide NAG A 610 bound to ASN A 341
19AE1SOFTWARETYR A:477 , ASN A:479 , ASN A:481 , GLU A:482 , THR A:483 , GLN A:484 , CSO B:66 , ASP B:87 , LEU B:88 , GLN B:270binding site for Poly-Saccharide residues NAG A 611 through NAG A 612 bound to ASN A 481
20AE2SOFTWAREASN A:486 , SER A:487 , THR A:488 , THR A:508binding site for Poly-Saccharide residues NAG A 613 through FUC A 615 bound to ASN A 486
21AE3SOFTWAREILE B:4 , ASN B:17binding site for Mono-Saccharide NAG B 601 bound to ASN B 17
22AE4SOFTWAREASN B:57binding site for Mono-Saccharide NAG B 602 bound to ASN B 57
23AE5SOFTWAREASN B:106 , ASN B:188 , HOH B:703binding site for Mono-Saccharide NAG B 603 bound to ASN B 106
24AE6SOFTWARETYR B:237 , ASN B:241 , ASN B:245 , TYR B:282 , FUL B:606 , HOH B:785binding site for Poly-Saccharide residues NAG B 604 through NAG B 605 bound to ASN B 241
25AE7SOFTWAREASN B:256 , GLU B:411binding site for Mono-Saccharide NAG B 607 bound to ASN B 256
26AE8SOFTWARESER B:338 , ASN B:341 , HOH B:701 , HOH B:716 , HOH B:744binding site for Mono-Saccharide NAG B 608 bound to ASN B 341
27AE9SOFTWARETYR A:237 , ARG A:240 , NAG A:607 , LYS B:427 , ASP B:454 , ASN B:455binding site for Poly-Saccharide residues NAG B 609 through FUC B 610 bound to ASN B 455
28AF1SOFTWARETYR B:477 , ASN B:481 , GLU B:482 , HOH B:756binding site for Mono-Saccharide NAG B 611 bound to ASN B 481

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:65 -A:92
2A:252 -A:263
3A:400 -A:519
4B:65 -B:92
5B:252 -B:263
6B:400 -B:519

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:101 -Pro A:102
2Gln A:380 -Arg A:381
3Ala B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DYT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DYT)

(-) Exons   (0, 0)

(no "Exon" information available for 5DYT)

(-) Sequences/Alignments

Asymmetric/Biological 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:527
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.eeeee..eeeeeeeeee.....hhhhh............eee..................hhhhhh............eeeeeee......eeeeeee...........hhhhhhhhhhhhhh.eeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhh.......eeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....................eeeee......eee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dyt A   3 DIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCcQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV 529
                                    12        22        32        42        52        62   |    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       
                                                                                          66-CSO                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.eeeee..eeeeeeeeee.....hhhhh............eee..................hhhhhh............eeeeeee......eeeeeee...........hhhhhhhhhhhhhh.eeeee....hhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhh......................hhhhhhhh.......eeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...................eeeee......eee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dyt B   4 IIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCcQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV 529
                                    13        23        33        43        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|      494       504       514       524     
                                                                                         66-CSO                                                                                                                                                                                                                                                                                                                                                                                                                          483|                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          485
   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 5DYT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DYT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DYT)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  5dyt
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  CHLE_HUMAN | P06276
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHLE_HUMAN | P06276: 1eho 1ehq 1kcj 1p0i 1p0m 1p0p 1p0q 1xlu 1xlv 1xlw 2j4c 2pm8 2wid 2wif 2wig 2wij 2wik 2wil 2wsl 2xmb 2xmc 2xmd 2xmg 2xqf 2xqg 2xqi 2xqj 2xqk 2y1k 3djy 3dkk 3o9m 4aqd 4axb 4b0o 4b0p 4bbz 4bds 4tpk 4xii 5dyw 5dyy 5k5e 5lkr

(-) Related Entries Specified in the PDB File

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