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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN S-ADENOSYLHOMOCYSTEINE HYDROLASE (AHCY) BOUND TO OXADIAZOLE INHIBITOR
 
Authors :  D. R. Dougan, J. D. Lawson, W. Lane
Date :  09 Jun 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Uchiyama, D. R. Dougan, J. D. Lawson, H. Kimura, S. I. Matsumoto, Y. Tanaka, T. Kawamoto
Identification Of Ahcy Inhibitors Using Novel High-Throughput Mass Spectrometry.
Biochem. Biophys. Res. 2017 Commun.
PubMed-ID: 28533090  |  Reference-DOI: 10.1016/J.BBRC.2017.05.107

(-) Compounds

Molecule 1 - ADENOSYLHOMOCYSTEINASE
    Chains: A, B
    EC Number: 3.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSX70
    Expression System Strain: ROSETTA 2(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AHCY, SAHH
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ADOHCYASE, S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
19W12Ligand/Ion(4-AMINO-1,2,5-OXADIAZOL-3-YL)[(3R)-3-{4-[(3-METHOXYPHENYL)AMINO]-6-METHYLPYRIDIN-2-YL}PYRROLIDIN-1-YL]METHANONE
2EDO14Ligand/Ion1,2-ETHANEDIOL
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (3, 36)
No.NameCountTypeFull Name
19W14Ligand/Ion(4-AMINO-1,2,5-OXADIAZOL-3-YL)[(3R)-3-{4-[(3-METHOXYPHENYL)AMINO]-6-METHYLPYRIDIN-2-YL}PYRROLIDIN-1-YL]METHANONE
2EDO28Ligand/Ion1,2-ETHANEDIOL
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:190 , ASN A:191 , GLY A:222 , ASP A:223 , VAL A:224 , THR A:242 , GLU A:243 , ILE A:244 , ASP A:245 , ASN A:248 , THR A:275 , THR A:276 , GLY A:277 , CYS A:278 , ILE A:281 , ILE A:299 , GLY A:300 , ASN A:346 , HOH A:649 , HOH A:650 , HOH A:652 , HOH A:671 , GLN B:413 , LYS B:426 , TYR B:430binding site for residue NAD A 501
02AC2SOFTWAREARG A:205 , LYS A:322 , PRO A:323 , CYS A:349 , HOH A:620binding site for residue EDO A 502
03AC3SOFTWAREMET A:210 , ALA A:212 , LYS A:214 , PHE B:356 , LYS B:401 , LEU B:402binding site for residue EDO A 503
04AC4SOFTWAREGLY A:284 , ARG A:285 , ASP A:307 , TRP A:310binding site for residue EDO A 504
05AC5SOFTWAREPHE A:356 , LYS A:401 , HOH A:626 , MET B:210 , ALA B:212 , LYS B:214binding site for residue EDO A 505
06AC6SOFTWAREVAL A:161 , ASN A:181 , ASP A:182 , HIS B:429binding site for residue EDO A 506
07AC7SOFTWAREASN A:320 , GLN A:324 , ASP A:326 , GLU A:341binding site for residue EDO A 507
08AC8SOFTWAREHIS A:55 , THR A:57 , GLU A:59 , THR A:60 , SER A:83 , GLN A:85 , LEU A:347 , ALA A:350 , MET A:351 , HIS A:353 , MET A:358 , PHE A:362binding site for residue 9W1 A 508
09AC9SOFTWAREGLY A:213 , VAL A:215 , ARG A:238 , TYR A:257 , LEU B:402binding site for residue EDO A 509
10AD1SOFTWARELEU A:409 , GLN A:413 , LYS A:426 , TYR A:430 , ASP B:190 , ASN B:191 , GLY B:222 , ASP B:223 , VAL B:224 , THR B:242 , GLU B:243 , ILE B:244 , ASP B:245 , ASN B:248 , THR B:275 , THR B:276 , GLY B:277 , CYS B:278 , ILE B:281 , ILE B:299 , GLY B:300 , HIS B:301 , ASN B:346 , 9W1 B:509 , HOH B:616 , HOH B:651 , HOH B:660 , HOH B:661 , HOH B:725 , HOH B:741 , HOH B:744binding site for residue NAD B 501
11AD2SOFTWARELEU B:283 , GLY B:284 , ARG B:285 , ASP B:307 , TRP B:310binding site for residue EDO B 502
12AD3SOFTWARELEU A:402 , ASN A:403 , GLY B:213 , VAL B:215 , ARG B:238 , ALA B:253 , TYR B:257 , GLU B:258 , HOH B:617binding site for residue EDO B 503
13AD4SOFTWAREGLU B:317 , VAL B:319 , ARG B:327 , ARG B:329 , HOH B:606binding site for residue EDO B 504
14AD5SOFTWARETHR A:207 , ASP A:208 , VAL A:209 , GLU B:28 , SER B:355 , HOH B:608 , HOH B:624 , HOH B:672binding site for residue EDO B 505
15AD6SOFTWARETRP B:17 , LYS B:20 , VAL B:316 , GLU B:317 , ARG B:329binding site for residue EDO B 506
16AD7SOFTWAREHIS A:429 , VAL B:161 , ASN B:181 , ASP B:182binding site for residue EDO B 507
17AD8SOFTWAREARG B:205 , LYS B:322 , PRO B:323 , CYS B:349binding site for residue EDO B 508
18AD9SOFTWAREHIS B:55 , THR B:57 , GLU B:59 , THR B:60 , SER B:83 , GLN B:85 , LEU B:347 , ALA B:350 , MET B:351 , HIS B:353 , MET B:358 , PHE B:362 , NAD B:501binding site for residue 9W1 B 509

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5W49)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:423 -Pro A:424
2Gly B:423 -Pro B:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5W49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5W49)

(-) Exons   (0, 0)

(no "Exon" information available for 5W49)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhh...ee.....hhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhhh....eeee........hhhhhh.....eeeee........hhhhhhhhh.eeeeee..eeeee.....eeeee.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhh.........hhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5w49 A   4 KLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIETLVTLGAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSCDGPFKPDHYRY 432
                                    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         


Chain B from PDB  Type:PROTEIN  Length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhh...ee.....hhhhhhhhhhh..........eeee..hhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhhh....eeee........hhhhhh.....eeeee........hhhhhhhhh.eeeeee..eeeee.....eeeee.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhh.........hhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5w49 B   4 KLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIETLVTLGAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSCDGPFKPDHYRY 432
                                    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
   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 5W49)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5W49)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5W49)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        SAHH_HUMAN | P23526: 1a7a 1li4 3nj4 4pfj 4pgf 4yvf 5w4b

(-) Related Entries Specified in the PDB File

5w4b