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(-) Description

Title :  CRYSTAL STRUCTURE OF APO CELL SHAPE DETERMINANT PROTEIN CSD4 FROM HELICOBACTER PYLORI
 
Authors :  A. C. Chan, M. E. Murphy
Date :  05 Sep 14  (Deposition) - 24 Dec 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Mixed Alpha Beta Sandwich, Carboxypeptidase, M14, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Chan, K. M. Blair, Y. Liu, E. Frirdich, E. C. Gaynor, M. E. Tanner, N. R. Salama, M. E. Murphy
Helical Shape Of Helicobacter Pylori Requires An Atypical Glutamine As A Zinc Ligand In The Carboxypeptidase Csd4.
J. Biol. Chem. V. 290 3622 2015
PubMed-ID: 25505267  |  Reference-DOI: 10.1074/JBC.M114.624734

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL SECRETED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B(MOD)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HPG27_353
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 563041
    Strain: G27

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 33)

Asymmetric/Biological Unit (2, 33)
No.NameCountTypeFull Name
1API1Ligand/Ion2,6-DIAMINOPIMELIC ACID
2IOD32Ligand/IonIODIDE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:135 , LYS A:319binding site for residue IOD A 502
02AC2SOFTWAREHIS A:263 , ASN A:267 , LYS A:329 , HOH A:738binding site for residue IOD A 504
03AC3SOFTWARELYS A:317binding site for residue IOD A 505
04AC4SOFTWARELYS A:325 , HOH A:838binding site for residue IOD A 506
05AC5SOFTWAREARG A:83binding site for residue IOD A 508
06AC6SOFTWAREHIS A:38 , HOH A:929binding site for residue IOD A 509
07AC7SOFTWARELYS A:163 , HOH A:897binding site for residue IOD A 510
08AC8SOFTWARETHR A:400 , HOH A:677binding site for residue IOD A 511
09AC9SOFTWAREPHE A:341binding site for residue IOD A 512
10AD1SOFTWAREGLN A:156 , ASP A:157 , ASN A:193 , ARG A:195 , GLN A:198binding site for residue IOD A 515
11AD2SOFTWAREILE A:301 , LYS A:317binding site for residue IOD A 516
12AD3SOFTWARELYS A:146binding site for residue IOD A 518
13AD4SOFTWARESER A:64 , HOH A:787binding site for residue IOD A 519
14AD5SOFTWAREARG A:380 , ASN A:427binding site for residue IOD A 520
15AD6SOFTWAREGLN A:156 , LYS A:160binding site for residue IOD A 522
16AD7SOFTWAREGLU A:158 , LYS A:404binding site for residue IOD A 523
17AD8SOFTWAREIOD A:527binding site for residue IOD A 524
18AD9SOFTWARELYS A:252 , ARG A:253 , HOH A:779binding site for residue IOD A 525
19AE1SOFTWARESER A:260binding site for residue IOD A 526
20AE2SOFTWAREPRO A:228 , SER A:231 , IOD A:524binding site for residue IOD A 527
21AE3SOFTWARESER A:19binding site for residue IOD A 528
22AE4SOFTWAREARG A:147 , HOH A:841binding site for residue IOD A 529
23AE5SOFTWARESER A:344 , LYS A:425 , HOH A:931binding site for residue IOD A 530
24AE6SOFTWARELYS A:300binding site for residue IOD A 531
25AE7SOFTWAREGLN A:303binding site for residue IOD A 532
26AE8SOFTWAREASN A:93 , ARG A:94 , HIS A:126 , HIS A:128 , MET A:203 , ALA A:206 , LEU A:207 , THR A:208 , ALA A:220 , GLU A:222 , HOH A:728 , HOH A:750 , HOH A:942 , HOH A:956binding site for residue API A 533

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WCK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WCK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WCK)

(-) 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee...hhhhhhhh.eeeee......hhhhhhhhhhhhhheee...eeeee...hhhhhhh.......hhhhh.........hhhhhhhhhhhhh.....eeeeeeee..ee........ee......eeee...........hhhhhhhhhhhhhhh...hhhhh.eeee.hhhhh..hhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhh....eeee.....ee......eeeeeeee...hhhhh.eee....eeeeee..eeeeee..eeeeeeeeeee.......eeeeee..eeeeee...eeee..eeee......eeee................eee.hhhhhhhh......eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wck A  19 SMEMIEKAPTDLEDRDKAPHLLLLAGIQGDEPGGFNATNLFLMHYSVLKGLVEVVPVLNKPSMLRNHRGLYGDMNRKFAALDKKDPEYPTIQEIKSLIAKPNIDAVLHLHDGGGYYRPVYVDAMLNPKRWGNCFIIDQDEVKGAKFPNLLAFANNTIESINAHLLHPIEEYHLKNTRTAQGDTEMQKALTFYAINQKKSAFANEASKELPLASRVFYHLQAIEGLLNQLNIPFKRDFELNPSSVHALINDKSLWAKISSLPKIPLFNLRPRLNHFPLPHNTKIPQIPIESNAYIVGLVKNKQEVFLKYGNKLMTRLSPFYIEFDPSLEEVKMQIDNKDQMVKIGSVVEVKESFYIHAMDNIRANVIGFSVSNENKPNEAGYTIRFKDFQKRFSLDKQERIYRIEFYKNNAFSGMILVKFV 438
                                    28        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       438
   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 4WCK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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        B5ZAD9_HELPG | B5ZAD9: 4wcl 4wcm 4wcn 5d2r

(-) Related Entries Specified in the PDB File

4wcl 4wcm 4wcn