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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-GALACTOSIDASE A IN COMPLEX WITH 1-DEOXYGALACTONOJIRIMYCIN-PFPHT
 
Authors :  J. L. Johnson, J. E. Drury, R. L. Lieberman
Date :  09 Dec 13  (Deposition) - 11 Jun 14  (Release) - 30 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pharmacological Chaperone, Drug Delivery Systems, Enzyme Activation, Enzyme Stability, Humans, Lysosomes, Molecular Chaperones, Protein Binding, Alpha-Galactosidase, Hydrolase-Hydrolase Inhibitor Complex, Fabry Disease, Gla Gene, Arylthiourea (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yu, T. Mena-Barragan, K. Higaki, J. L. Johnson, J. E. Drury, R. L. Lieberman, N. Nakasone, H. Ninomiya, T. Tsukimura, H. Sakuraba, Y. Suzuki, E. Nanba, C. O. Mellet, J. M. Garcia Fernandez, K. Ohno
Molecular Basis Of 1-Deoxygalactonojirimycin Arylthiourea Binding To Human Alpha-Galactosidase A: Pharmacological Chaperoning Efficacy On Fabry Disease Mutants.
Acs Chem. Biol. V. 9 1460 2014
PubMed-ID: 24783948  |  Reference-DOI: 10.1021/CB500143H

(-) Compounds

Molecule 1 - ALPHA-GALACTOSIDASE A
    Chains: A, B
    EC Number: 3.2.1.22
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Gene: GLA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-D-GALACTOSIDASE A, ALPHA-D-GALACTOSIDE GALACTOHYDROLASE, MELIBIASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
12OZ2Ligand/Ion(2R,3S,4R,5S)-N-(4-FLUOROPHENYL)-3,4,5-TRIHYDROXY-2-(HYDROXYMETHYL)PIPERIDINE-1-CARBOTHIOAMIDE
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO45Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:332 , ILE A:367 , ALA A:368 , SER A:371 , ARG A:402BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWARELYS A:237 , HOH A:604 , HOH A:612 , TRP B:236 , LYS B:237BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWARELEU A:32 , ASP A:33 , ARG A:220BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREASP A:33 , ASN A:34 , ASN A:192 , NAG A:505 , PRO B:210BINDING SITE FOR RESIDUE NAG A 504
05AC5SOFTWAREASP A:33 , NAG A:504 , LYS B:213BINDING SITE FOR RESIDUE NAG A 505
06AC6SOFTWAREASN A:139 , PHE A:149 , TYR A:173 , CYS A:174 , ASP A:175 , ASN A:179BINDING SITE FOR RESIDUE NAG A 506
07AC7SOFTWAREASN A:215 , THR A:217 , GLU A:218 , HOH A:650BINDING SITE FOR RESIDUE NAG A 507
08AC8SOFTWARETRP A:47 , ASP A:92 , ASP A:93 , TYR A:134 , CYS A:142 , LYS A:168 , ASP A:170 , GLU A:203 , LEU A:206 , TYR A:207 , ARG A:227 , ASP A:231BINDING SITE FOR RESIDUE 2OZ A 508
09AC9SOFTWAREARG B:332 , ILE B:367 , ALA B:368 , SER B:371 , ARG B:402BINDING SITE FOR RESIDUE SO4 B 501
10BC1SOFTWARESER B:401 , ARG B:402 , ARG B:404BINDING SITE FOR RESIDUE SO4 B 502
11BC2SOFTWAREASP B:33 , ASN B:34 , ASN B:192 , ARG B:196 , NAG B:504 , HOH B:638BINDING SITE FOR RESIDUE NAG B 503
12BC3SOFTWARENAG B:503BINDING SITE FOR RESIDUE NAG B 504
13BC4SOFTWAREASN B:215 , THR B:217 , GLU B:218BINDING SITE FOR RESIDUE NAG B 505
14BC5SOFTWAREASN B:139 , PHE B:149 , TYR B:173 , CYS B:174 , ASP B:175BINDING SITE FOR RESIDUE NAG B 506
15BC6SOFTWAREARG A:193 , TRP B:47 , ASP B:92 , ASP B:93 , TYR B:134 , CYS B:142 , LYS B:168 , ASP B:170 , GLU B:203 , LEU B:206 , TYR B:207 , ARG B:227 , ASP B:231BINDING SITE FOR RESIDUE 2OZ B 507

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:52 -A:94
2A:56 -A:63
3A:142 -A:172
4A:202 -A:223
5A:378 -A:382
6B:52 -B:94
7B:56 -B:63
8B:142 -B:172
9B:202 -B:223
10B:378 -B:382

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:379 -Pro A:380
2Leu A:388 -Pro A:389
3Asn B:379 -Pro B:380
4Leu B:388 -Pro B:389

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NXS)

(-) 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:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeehhhhhh.............hhhhhhhhhhhhhhh........eee.........................hhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhh.....eeee............hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhh.......eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh.......eeeeee..eeeeeee....eeeeeeee.......eeeeee.hhhhhhh....eeeeeeee...eeeeeee...eeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nxs A  32 LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENTM 421
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421


Chain B from PDB  Type:PROTEIN  Length:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeehhhhhh.............hhhhhhhhhhhhhhh........eee........................hhhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhh.....eeee............hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhh.......eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh.......eeeeee..eeeeeee....eeeeeeee.......eeeeee.hhhhhhh....eeeeeeee...eeeeeee...eeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nxs B  32 LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENTMQ 422
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421
   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 4NXS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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        AGAL_HUMAN | P06280: 1r46 1r47 3gxn 3gxp 3gxt 3hg2 3hg3 3hg4 3hg5 3lx9 3lxa 3lxb 3lxc 3s5y 3s5z 3tv8

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