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(-) Description

Title :  CRYSTAL STRUCTURE OF TRIPEPTIDE BOUND CELL SHAPE DETERMINANT CSD4 PROTEIN 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 :  1.75
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, 45)

Asymmetric/Biological Unit (4, 45)
No.NameCountTypeFull Name
13KS1Ligand/IonN-ACETYL-L-ALANYL-N-[(1S,5R)-5-AMINO-1,5-DICARBOXYPENTYL]-D-GLUTAMINE
2IOD41Ligand/IonIODIDE ION
3NA2Ligand/IonSODIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:319 , NA A:544binding site for residue IOD A 502
02AC2SOFTWAREASN A:166binding site for residue IOD A 503
03AC3SOFTWAREHIS A:263 , ASN A:267 , LYS A:329binding site for residue IOD A 504
04AC4SOFTWARELYS A:317binding site for residue IOD A 505
05AC5SOFTWARETHR A:400binding site for residue IOD A 511
06AC6SOFTWAREPHE A:341binding site for residue IOD A 512
07AC7SOFTWAREGLN A:320binding site for residue IOD A 513
08AC8SOFTWAREHIS A:292binding site for residue IOD A 514
09AC9SOFTWAREASN A:193 , ARG A:195binding site for residue IOD A 515
10AD1SOFTWARESER A:64 , HOH A:705binding site for residue IOD A 518
11AD2SOFTWAREARG A:409binding site for residue IOD A 519
12AD3SOFTWARETYR A:89 , ARG A:147binding site for residue IOD A 520
13AD4SOFTWAREIOD A:528binding site for residue IOD A 524
14AD5SOFTWAREARG A:253binding site for residue IOD A 525
15AD6SOFTWAREARG A:253 , GLU A:256 , LEU A:257binding site for residue IOD A 526
16AD7SOFTWARESER A:260binding site for residue IOD A 527
17AD8SOFTWARESER A:231 , IOD A:524 , HOH A:811binding site for residue IOD A 528
18AD9SOFTWARESER A:19binding site for residue IOD A 529
19AE1SOFTWAREARG A:147 , 3KS A:545binding site for residue IOD A 530
20AE2SOFTWARELYS A:269binding site for residue IOD A 531
21AE3SOFTWARESER A:344 , LYS A:425binding site for residue IOD A 532
22AE4SOFTWARELYS A:300binding site for residue IOD A 533
23AE5SOFTWAREGLN A:303 , NA A:543binding site for residue IOD A 534
24AE6SOFTWAREGLN A:351 , ASN A:354 , SER A:370binding site for residue IOD A 535
25AE7SOFTWARELYS A:404 , HOH A:913binding site for residue IOD A 536
26AE8SOFTWAREALA A:26 , VAL A:65binding site for residue IOD A 540
27AE9SOFTWARESER A:276 , PRO A:296 , PRO A:305binding site for residue IOD A 541
28AF1SOFTWAREGLN A:46 , GLU A:49 , HIS A:128 , HOH A:687binding site for residue ZN A 542
29AF2SOFTWARELYS A:300 , PRO A:302 , IOD A:534binding site for residue NA A 543
30AF3SOFTWAREARG A:135 , IOD A:502 , HOH A:640binding site for residue NA A 544
31AF4SOFTWAREARG A:86 , ASN A:93 , ARG A:94 , HIS A:126 , HIS A:128 , GLY A:130 , GLY A:131 , TRP A:148 , MET A:203 , ALA A:206 , LEU A:207 , THR A:208 , ALA A:220 , GLU A:222 , LYS A:225 , IOD A:530 , HOH A:678 , HOH A:683 , HOH A:792 , HOH A:927binding site for residue 3KS A 545

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WCN)

(-) 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:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee...hhhhhhhh.eeeee......hhhhhhhhhhhhhheee...eeeee...hhhhhhh.......hhhhh.........hhhhhhhhhhhhhh....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......eeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wcn A  19 SMEMIEKAPTDLEDRDKAPHLLLLAGIQGDEPGGFNATNLFLMHYSVLKGLVEVVPVLNKPSMLRNHRGLYGDMNRKFAALDKKDPEYPTIQEIKSLIAKPNIDAVLHLHDGGGYYRPVYVDAMLNPKRWGNCFIIDQDEVKGAKFPNLLAFANNTIESINAHLLHPIEEYHLKNTRTAQGDTEMQKALTFYAINQKKSAFANEASKELPLASRVFYHLQAIEGLLNQLNIPFKRDFELNPSSVHALINDKSLWAKISSLPKIPLFNLRPRLNHFPLPHNTKIPQIPIESNAYIVGLVKNKQEVFLKYGNKLMTRLSPFYIEFDPSLEEVKMQIDNKDQMVKIGSVVEVKESFYIHAMDNIRANVIGFSVNEAGYTIRFKDFQKRFSLDKQERIYRIEFYKNNAFSGMILVKFV 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|      404       414       424       434    
                                                                                                                                                                                                                                                                                                                                                                                                           388|                                           
                                                                                                                                                                                                                                                                                                                                                                                                            395
   Legend:   → Mismatch (orange background)
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  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 4WCN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

4wck 4wcl 4wcm