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(-) Description

Title :  STRUCTURAL ANALYSIS OF THE APO-FORM 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 :  1.60
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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:46 , GLU A:49 , HIS A:128 , HOH A:635 , HOH A:740 , HOH A:789BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREASN A:382 , VAL A:383 , PHE A:386 , GLU A:396 , HOH A:692 , HOH A:730BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREHIS A:62 , ASP A:254 , HOH A:802BINDING SITE FOR RESIDUE CA A 503
4AC4SOFTWAREASN A:93 , ALA A:206 , GLU A:222 , HOH A:789 , HOH A:981 , HOH A:1031BINDING SITE FOR RESIDUE GOL A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q6M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q6M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q6M)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q6M)

(-) 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...hhhhhhh..eeeee......hhhhhhhhhhhhhheee...eeeee...hhhhhhh.......hhhhh.........hhhhhhhhhhhhh.....eeeeeeee..ee........ee......eeee...........hhhhhhhhhhhhhhh...hhhhh.eeee.hhhhhhhhhh.hhhhhhhhh..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
                 4q6m 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 4Q6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q6M)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        O25708_HELPY | O25708: 4q6n 4q6o 4q6p 4q6q

(-) Related Entries Specified in the PDB File

4q6n 4q6o 4q6p 4q6q