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(-) Description

Title :  STRUCTURAL ANALYSIS OF THE ZN-FORM II OF HELICOBACTER PYLORI CSD4, A D,L-CARBOXYPEPTIDASE
 
Authors :  H. S. Kim, J. Kim, H. N. Im, D. R. An, M. Lee, D. Hesek, S. Mobashery, J. Y. Ki H. J. Yoon, B. W. Han, B. I. Lee, S. W. Suh
Date :  23 Apr 14  (Deposition) - 05 Nov 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  M14 Metallopeptidase, D, L-Carboxypeptidase, Peptidoglycan, Csd5, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Kim, J. Kim, H. N. Im, D. R. An, M. Lee, D. Hesek, S. Mobashery, J. Y. Kim, K. Cho, H. J. Yoon, B. W. Han, B. I. Lee, S. W. Suh
Structural Basis For The Recognition Of Muramyltripeptide B Helicobacter Pylori Csd4, A D, L-Carboxypeptidase Controllin The Helical Cell Shape
Acta Crystallogr. , Sect. D V. 70 2800 2014
PubMed-ID: 25372672  |  Reference-DOI: 10.1107/S1399004714018732

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL SECRETED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 22-438
    Gene: HP_1075
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: ATCC 700392
    Synonym: CSD4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1API1Ligand/Ion2,6-DIAMINOPIMELIC ACID
2CA2Ligand/IonCALCIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:796 , HOH A:797 , HOH A:798BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREASN A:382 , VAL A:383 , PHE A:386 , GLU A:396 , HOH A:636 , HOH A:665BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREASN A:173 , GLU A:176 , GLY A:398 , HOH A:674 , HOH A:773 , HOH A:787 , HOH A:813BINDING SITE FOR RESIDUE CA A 504
4AC4SOFTWAREASN 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:623 , HOH A:630BINDING SITE FOR RESIDUE API A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q6Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q6Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q6Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q6Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q6Q)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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..eeeeeeeeeeeee.....eeeeee..eeeeee...eeee..eeee......eeee................eee.hhhhhhhh......eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q6q A  22 MIEKAPTNVEDRDKAPHLLLLAGIQGDEPGGFNATNLFLMHYSVLKGLVEVVPVLNKPSMLRNHRGLYGDMNRKFAALDKNDPEYPTIQEIKSLIAKPSIDAVLHLHDGGGYYRPVYVDAMLNPKRWGNCFIIDQDEVKGAKFPNLLAFANNTIESINAHLLHPIEEYHLKNTRTAQGDTEMQKALTFYAINQKKSAFANEASKELPLASRVFYHLQAIEGLLNQLNIPFKRDFDLNPNSVHALINDKNLWAKISSLPKMPLFNLRPKLNHFPLPHNTKIPQIPIESNAYIVGLVKNKQEVFLKYGNKLMTRLSPFYIEFDPSLEEVKMQIDNKDQMVKIGSVVEVKESFYIHAMDNIRANVIGFSVSNENKPNEAGYTIKFKDFQKRFSLDKQERIYRIEFYKNNAFSGMILVKFV 438
                                    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
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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 4Q6Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q6Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q6Q)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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        O25708_HELPY | O25708: 4q6m 4q6n 4q6o 4q6p

(-) Related Entries Specified in the PDB File

4q6m 4q6n 4q6o 4q6p