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(-) Description

Title :  STRUCTURE OF VIBRIO CHOLERAE CHITIN DE-N-ACETYLASE IN COMPLEX WITH 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE (NDG) AND ZINC ION
 
Authors :  D. Albesa-Jove, E. Andres, X. Biarnes, A. Planas, M. E. Guerin
Date :  11 Dec 13  (Deposition) - 13 Aug 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B
Keywords :  (Beta/Alpha)7, Carbohydrate Esterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Andres, D. Albesa-Jove, X. Biarnes, B. M. Moerschbacher, M. E. Guerin, A. Planas
Structural Basis Of Chitin Oligosaccharide Deacetylation.
Angew. Chem. Int. Ed. Engl. V. 53 6882 2014
PubMed-ID: 24810719  |  Reference-DOI: 10.1002/ANIE.201400220

(-) Compounds

Molecule 1 - DEACETYLASE DA1
    Chains: A, B
    EC Number: 3.5.1.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 23-427
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 1095658

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3GOL4Ligand/IonGLYCEROL
4NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5ZN2Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:40 , HIS A:97 , HIS A:101 , ACT A:503 , HOH A:605BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREGLY A:223 , GLY A:355 , HOH A:601 , HOH A:602 , HOH A:603 , HOH A:604BINDING SITE FOR RESIDUE CA A 502
03AC3SOFTWAREASP A:39 , ASP A:40 , HIS A:97 , HIS A:101 , PRO A:168 , TYR A:169 , TRP A:229 , HIS A:295 , ZN A:501BINDING SITE FOR RESIDUE ACT A 503
04AC4SOFTWAREASP A:40 , HIS A:101 , ASN A:119 , HIS A:124 , ARG A:304 , HOH A:606 , HOH A:607 , HOH A:608 , HOH A:698 , HOH A:838BINDING SITE FOR RESIDUE NDG A 504
05AC5SOFTWAREGLU A:140 , LEU A:143 , TYR A:162 , GLN A:222 , HOH A:650 , HOH A:746 , HOH A:762 , ARG B:154 , GOL B:505 , HOH B:740 , HOH B:796BINDING SITE FOR RESIDUE GOL A 505
06AC6SOFTWAREASP B:40 , HIS B:97 , HIS B:101 , ACT B:503 , HOH B:604BINDING SITE FOR RESIDUE ZN B 501
07AC7SOFTWAREGLY B:223 , GLY B:355 , HOH B:601 , HOH B:602 , HOH B:603 , HOH B:750BINDING SITE FOR RESIDUE CA B 502
08AC8SOFTWAREASP B:39 , ASP B:40 , HIS B:97 , HIS B:101 , PRO B:168 , TYR B:169 , TRP B:229 , HIS B:295 , ZN B:501BINDING SITE FOR RESIDUE ACT B 503
09AC9SOFTWAREASP B:40 , HIS B:101 , ASN B:119 , HIS B:124 , PHE B:297 , ARG B:304 , HOH B:605 , HOH B:606 , HOH B:638 , HOH B:657 , HOH B:753BINDING SITE FOR RESIDUE NDG B 504
10BC1SOFTWAREGOL A:505 , HOH A:661 , GLU B:140 , TYR B:162 , GLN B:222 , HOH B:617 , HOH B:639 , HOH B:796BINDING SITE FOR RESIDUE GOL B 505
11BC2SOFTWAREASN A:221 , ASN A:387 , ASN A:401 , HOH A:662 , PRO B:151 , THR B:152 , ARG B:154 , SER B:155 , HOH B:711BINDING SITE FOR RESIDUE GOL B 506
12BC3SOFTWARELEU B:285 , PRO B:337 , GLU B:349 , TYR B:350 , HOH B:748 , HOH B:826BINDING SITE FOR RESIDUE GOL B 507

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:106 -A:118
2A:185 -A:200
3A:264 -A:281
4B:106 -B:118
5B:185 -B:200
6B:264 -B:281

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:41 -Pro A:42
2Glu A:270 -Pro A:271
3Gly B:41 -Pro B:42
4Glu B:270 -Pro B:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4NZ4)

(-) 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:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhhh...eeeehhhhh.........hhhhhhhhhhhh..eeee.....hhhhh......hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.hhhhh.......ee.......eeee..eee........................hhhhhhhhhhhhhhhhh..ee....ee.........hhhhhh.hhhhhhhhhhhhh..hhhhhh.hhhhh.......hhhhh.eeeeeee.hhh.ee..eehhhhhhhhhhhhhhhhhhh.eeee.............ee....eeee..eeeee...ee.hhhhh.......eee...........ee....eeee..eeeee...ee.............eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nz4 A  29 TPKGTIYLTFDDGPVNASVEVIKVLNQGGVKATFYFNAWHLDGIGDENEDRALEALKLALDSGHIVGNHSYDHMIHNCVEEFGPTSGADCNATGNHQIHSYQDPVRDAASFEQNLITLEKYLPTIRSYPNYKGYELARLPYTNGWRVTKHFQADGLCATSDNLKPWEPGYVCDPANPSNSVKASIQVQNILANQGYQTHGWDVDWAPENWGIPMPANSLTEAVPFLAYVDKALNSCSPTTIEPINSKTQEFPCGTPLHADKVIVLTHDFLFEDGKRGMGATQNLPKLAEFIRIAKEAGYVFDTMDNYTPRWSVGKTYQAGEYVLYQGVVYKAVISHTAQQDWAPSSTSSLWTNADPATNWTLNVSYEQGDIVNYKGKRYLVSVPHVSQQDWTPDTQNTLFTALE 432
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428    


Chain B from PDB  Type:PROTEIN  Length:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhhh...eeeehhhhhhh.......hhhhhhhhhhhh..eeee.....hhhhh......hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.hhhhh.......ee.......eeee..eee........................hhhhhhhhhhhhhhhhh..ee....ee.........hhhhhh.hhhhhhhhhhhhh..hhhhhh.hhhhh.......hhhhh.eeeeeee.hhh.ee..eehhhhhhhhhhhhhhhhhhh.eee.hhhhh........ee....eeee..eeeee...ee.............eee...........ee....eeee..eeeee...ee.............eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nz4 B  29 TPKGTIYLTFDDGPVNASVEVIKVLNQGGVKATFYFNAWHLDGIGDENEDRALEALKLALDSGHIVGNHSYDHMIHNCVEEFGPTSGADCNATGNHQIHSYQDPVRDAASFEQNLITLEKYLPTIRSYPNYKGYELARLPYTNGWRVTKHFQADGLCATSDNLKPWEPGYVCDPANPSNSVKASIQVQNILANQGYQTHGWDVDWAPENWGIPMPANSLTEAVPFLAYVDKALNSCSPTTIEPINSKTQEFPCGTPLHADKVIVLTHDFLFEDGKRGMGATQNLPKLAEFIRIAKEAGYVFDTMDNYTPRWSVGKTYQAGEYVLYQGVVYKAVISHTAQQDWAPSSTSSLWTNADPATNWTLNVSYEQGDIVNYKGKRYLVSVPHVSQQDWTPDTQNTLFTALE 432
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428
   Legend:   → Mismatch (orange background)
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  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 4NZ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NZ4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4NZ4)

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(-) Related Entries Specified in the PDB File

4ny2 4nyu 4nyy 4nz1 4nz3 4nz5