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(-) Description

Title :  CRYSTAL STRUCTURE OF PRODUCT BOUND 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 :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Mixed Alpha Beta Sandwich, Carboxypeptidase, M14 (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  (4, 36)

Asymmetric/Biological Unit (4, 36)
No.NameCountTypeFull Name
1API1Ligand/Ion2,6-DIAMINOPIMELIC ACID
2IOD31Ligand/IonIODIDE ION
3NA1Ligand/IonSODIUM ION
4ZN3Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:62 , ASP A:254 , HOH A:778 , HOH A:962binding site for residue ZN A 501
02AC2SOFTWAREGLN A:46 , GLU A:49 , HIS A:128 , HOH A:702 , HOH A:746binding site for residue ZN A 502
03AC3SOFTWAREMET A:358 , IOD A:526 , IOD A:527 , IOD A:532binding site for residue ZN A 503
04AC4SOFTWAREGLN A:303binding site for residue IOD A 504
05AC5SOFTWAREARG A:83binding site for residue IOD A 505
06AC6SOFTWAREHIS A:263 , ASN A:267 , LYS A:329binding site for residue IOD A 506
07AC7SOFTWARELYS A:317binding site for residue IOD A 508
08AC8SOFTWARELYS A:319binding site for residue IOD A 511
09AC9SOFTWAREPHE A:341binding site for residue IOD A 513
10AD1SOFTWAREGLN A:198binding site for residue IOD A 514
11AD2SOFTWAREARG A:147binding site for residue IOD A 515
12AD3SOFTWARESER A:64 , HOH A:889binding site for residue IOD A 516
13AD4SOFTWAREPRO A:119binding site for residue IOD A 517
14AD5SOFTWAREGLU A:187binding site for residue IOD A 518
15AD6SOFTWARELYS A:325binding site for residue IOD A 521
16AD7SOFTWARENA A:536binding site for residue IOD A 522
17AD8SOFTWAREZN A:503binding site for residue IOD A 526
18AD9SOFTWARELYS A:349 , ZN A:503binding site for residue IOD A 527
19AE1SOFTWARESER A:19binding site for residue IOD A 529
20AE2SOFTWARESER A:260binding site for residue IOD A 530
21AE3SOFTWARELYS A:349 , ZN A:503binding site for residue IOD A 532
22AE4SOFTWARETHR A:400 , HOH A:641binding site for residue IOD A 534
23AE5SOFTWAREASN A:93 , ARG A:94 , HIS A:126 , HIS A:128 , TRP A:148 , MET A:203 , ALA A:206 , LEU A:207 , THR A:208 , ALA A:220 , GLU A:222 , HOH A:706 , HOH A:726 , HOH A:754 , HOH A:764binding site for residue API A 535
24AE6SOFTWAREHIS A:38 , IOD A:522binding site for residue NA A 536

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:426 -Asn A:427

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WCL)

(-) 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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..hhhhhhhhhhhh...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
                 4wcl A  19 SMEMIEKAPTDLEDRDKAPHLLLLAGIQGDEPGGFNATNLFLMHYSVLKGLVEVVPVLNKPSMLRNHRGLYGDMNRKFAALDKKDPEYPTIQEIKSLIAKPNIDAVLHLHDGGGYYRPVYVDAMLNPKRWGNCFIIDQDEVKGAKFPNLLAFANNTIESINAHLLHPIEEYHLKNTRTAQGDTEMQKALTFYAINQKKSAFANEASKELPLASRVFYHLQAIEGLLNQLNIPFKRDFELNPSSVHALINDKSLWAKISSLPKIPLFNLRPRLNHFPLPHNTKIPQIPIESNAYIVGLVKNKQEVFLKYGNKLMTRLSPFYIEFDPSLEEVKMQIDNKDQMVKIGSVVEVKESFYIHAMDNIRANVIGFSVKPNEAGYTIRFKDFQKRFSLDKQERIYRIEFYKNNAFSGMILVKFV 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|      402       412       422       432      
                                                                                                                                                                                                                                                                                                                                                                                                           388|                                             
                                                                                                                                                                                                                                                                                                                                                                                                            393
   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 4WCL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

4wck 4wcm 4wcn