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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF CHITINASE A FROM VIBRIO HARVEYI WITH NOVEL INHIBITORS - COMPLEX STRUCTURE WITH DEQUALINIUM
 
Authors :  S. Pantoom, I. R. Vetter, H. Prinz, W. Suginta
Date :  09 Dec 10  (Deposition) - 20 Apr 11  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Inhibitor Complex, Glycosidase, Hydrolase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pantoom, I. R. Vetter, H. Prinz, W. Suginta
Potent Family-18 Chitinase Inhibitors: X-Ray Structures, Affinities, And Binding Mechanisms
J. Biol. Chem. V. 286 24312 2011
PubMed-ID: 21531720  |  Reference-DOI: 10.1074/JBC.M110.183376
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITINASE A
    Chains: A
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 22-597
    Gene: CHIA
    Organism Scientific: VIBRIO HARVEYI
    Organism Taxid: 669
    Strain: LMG7890

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1DEQ1Ligand/IonDEQUALINIUM
2GOL3Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:168 , SER A:209 , TRP A:275 , THR A:276 , TRP A:397 , ARG A:463 , HOH A:885 , GOL A:3500BINDING SITE FOR RESIDUE DEQ A 606
2AC2SOFTWAREPHE A:316 , GLY A:365 , VAL A:366 , GLY A:367 , LYS A:370 , MET A:389 , TYR A:391 , DEQ A:606 , HOH A:1027 , HOH A:1034BINDING SITE FOR RESIDUE GOL A 3500
3AC3SOFTWAREGLU A:114 , CYS A:121 , SER A:122 , LYS A:123 , GLY A:206 , GLY A:207 , ASN A:211 , HOH A:637 , HOH A:927 , HOH A:1243BINDING SITE FOR RESIDUE GOL A 3501
4AC4SOFTWARELYS A:151 , HIS A:549 , ASP A:578 , ASN A:581 , ALA A:582 , GLU A:585 , HOH A:614 , HOH A:1101 , HOH A:1319BINDING SITE FOR RESIDUE GOL A 3502

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:116 -A:121
2A:196 -A:217
3A:409 -A:418

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:191 -Phe A:192
2Glu A:315 -Phe A:316
3Trp A:570 -Glu A:571

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ARP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ARP)

(-) Exons   (0, 0)

(no "Exon" information available for 3ARP)

(-) 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:574
 aligned with Q9AMP1_VIBHA | Q9AMP1 from UniProtKB/TrEMBL  Length:850

    Alignment length:574
                                    31        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       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591    
         Q9AMP1_VIBHA    22 APTAPSIDMYGSNNLQFSKIELAMETTSGYNDMVKYHELAKIKVKFNQWSGTSGDTYNVYFDGVKVATGAITGSQTTASFEYGQGGLYQMEIEACDATGCSKSAPVEITIADTDGSHLKPLTMNVDPNNKSYNTDPSIVMGTYFVEWGIYGRDYTVDNMPVDNLTHILYGFIPICGPNESVKSVGGNSFNALQTACRGVNDYEVVIHDPWAAYQKSFPQAGHEYSTPIKGNYAMLMALKQRNPDLKIIPSIGGWTLSDPFYDFVDKKNRDTFVASVKKFLKTWKFYDGVDIDWEFPGGGGAAADKGDPVNDGPAYIALMRELRVMLDELEAETGRTYELTSAIGVGYDKIEDVDYADAVQYMDYIFAMTYDFYGGWNNVPGHQTALYCGSFMRPGQCDGGGVDENGEPYKGPAYTADNGIQLLLAQGVPANKLVLGTAMYGRGWEGVTPDTLTDPNDPMTGTATGKLKGSTAQGVWEDGVIDYKGIKSFMLGANNTGINGFEYGYDAQAEAPWVWNRSTGELITFDDHRSVLAKGNYAKSLGLAGLFSWEIDADNGDILNAMHEGMAGGVVTPP 595
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhh.eee.eee......hhhhheee...eeeeeeee........eeeeee..eeeeeee....eeeeeeee...eeeeeeeeeee..eeee...eeeeee...........................eeeeeee.hhhh....hhhhhhhhhh.eeeeeee.....hhhhhhhh.hhhhhhhhhh...........hhhhhhh..hhhhh.......hhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee................hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh..hhhhhhhhh.eeeee..............................................hhhhhhhhhhhh..hhh.eeeeee.eeeeee..hhhhh....hhhhh...ee...hhhhh.....eeehhhhhhhh...........eeeee....eeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3arp A  22 APTAPSIDMYGSNNLQFSKIELAMETTSGYNDMVKYHELAKIKVKFNQWSGTSGDTYNVYFDGVKVATGAITGSQTTASFEYGQGGLYQMEIEACDATGCSKSAPVEITIADTDGSHLKPLTMNVDPNNKSYNTDPSIVMGTYFVEWGIYGRDYTVDNMPVDNLTHILYGFIPICGPNESVKSVGGNSFNALQTACRGVNDYEVVIHDPWAAYQKSFPQAGHEYSTPIKGNYAMLMALKQRNPDLKIIPSIGGWTLSDPFYDFVDKKNRDTFVASVKKFLKTWKFYDGVDIDWEFPGGGGAAADKGDPVNDGPAYIALMRELRVMLDELEAETGRTYELTSAIGVGYDKIEDVDYADAVQYMDYIFAMTYDFYGGWNNVPGHQTALYCGSFMRPGQCDGGGVDENGEPYKGPAYTADNGIQLLLAQGVPANKLVLGTAMYGRGWEGVTPDTLTDPNDPMTGTATGKLKGSTAQGVWEDGVIDYKGIKSFMLGANNTGINGFEYGYDAQAEAPWVWNRSTGELITFDDHRSVLAKGNYAKSLGLAGLFSWEIDADNGDILNAMHEGMAGGVVTPP 595
                                    31        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       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591
   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 3ARP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ARP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ARP)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9AMP1_VIBHA | Q9AMP1)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  3.2.1.14
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 Related Entries

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

UniProtKB/TrEMBL
        Q9AMP1_VIBHA | Q9AMP1: 3aro 3arq 3arr 3ars 3art 3aru 3arv 3arw 3arx 3ary 3arz 3as0 3as1 3as2 3as3 3b8s 3b9a 3b9d 3b9e

(-) Related Entries Specified in the PDB File

3aro 3arq 3arr 3ars 3art 3aru 3arv 3arw 3arx 3ary 3arz 3as0 3as1 3as2 3as3