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(-) Description

Title :  CRYSTAL STRUCTURE OF ZIPA IN COMPLEX WITH AN INHIBITOR
 
Authors :  L. Mosyak, T. S. Rush
Date :  22 Nov 04  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Rush, J. A. Grant, L. Mosyak, A. Nicholls
A Shape-Based 3-D Scaffold Hopping Method And Its Application To A Bacterial Protein-Protein Interaction
J. Med. Chem. V. 48 1489 2005
PubMed-ID: 15743191  |  Reference-DOI: 10.1021/JM040163O
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELL DIVISION PROTEIN ZIPA
    Chains: A, B
    Engineered: YES
    Gene: ZIPA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CL31Ligand/IonN-METHYL-N-[3-(6-PHENYL[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-3-YL)PHENYL]ACETAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL31Ligand/IonN-METHYL-N-[3-(6-PHENYL[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-3-YL)PHENYL]ACETAMIDE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL3-1Ligand/IonN-METHYL-N-[3-(6-PHENYL[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-3-YL)PHENYL]ACETAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:12 , MET A:42 , ILE A:44 , ALA A:62 , PRO A:67 , GLY A:68 , PHE A:85BINDING SITE FOR RESIDUE CL3 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y2G)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:66 -Pro A:67
2Val A:88 -Pro A:89
3Lys B:66 -Pro B:67
4Val B:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y2G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y2G)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y2G)

(-) Sequences/Alignments

Asymmetric 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:137
 aligned with ZIPA_ECOLI | P77173 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:137
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       
           ZIPA_ECOLI   190 RKEAVIIMNVAAHHGSELNGELLLNSIQQAGFIFGDMNIYHRHLSPDGSGPALFSLANMVKPGTFDPEMKDFTTPGVTIFMQVPSYGDELQNFKLMLQSAQHIADEVGGVVLDDQRRMMTPQKLREYQDIIREVKDA 326
               SCOP domains d1y2ga_ A: automated matches                                                                                                              SCOP domains
               CATH domains 1y2gA00 A:6-142  [code=3.30.1400.10, no name defined]                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......eehhhhhhhhhhh..ee.hhh.eeee........eeeeeee..............ee.eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2g A   6 RKEAVIIMNVAAHHGSELNGELLLNSIQQAGFIFGDMNIYHRHLSPDGSGPALFSLANMVKPGTFDPEMKDFTTPGVTIFMQVPSYGDELQNFKLMLQSAQHIADEVGGVVLDDQRRMMTPQKLREYQDIIREVKDA 142
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with ZIPA_ECOLI | P77173 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:140
                                   198       208       218       228       238       248       258       268       278       288       298       308       318       328
           ZIPA_ECOLI   189 KRKEAVIIMNVAAHHGSELNGELLLNSIQQAGFIFGDMNIYHRHLSPDGSGPALFSLANMVKPGTFDPEMKDFTTPGVTIFMQVPSYGDELQNFKLMLQSAQHIADEVGGVVLDDQRRMMTPQKLREYQDIIREVKDANA 328
               SCOP domains d1y2gb_ B: automated matches                                                                                                                 SCOP domains
               CATH domains 1y2gB00 B:5-144  [code=3.30.1400.10, no name defined]                                                                                        CATH domains
           Pfam domains (1) --ZipA_C-1y2gB01 B:7-136                                                                                                            -------- Pfam domains (1)
           Pfam domains (2) --ZipA_C-1y2gB02 B:7-136                                                                                                            -------- Pfam domains (2)
         Sec.struct. author ....eeeeeeee......eehhhhhhhhhhh..eeehhheeeee........eeeeeee..............ee.eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2g B   5 KRKEAVIIMNVAAHHGSELNGELLLNSIQQAGFIFGDMNIYHRHLSPDGSGPALFSLANMVKPGTFDPEMKDFTTPGVTIFMQVPSYGDELQNFKLMLQSAQHIADEVGGVVLDDQRRMMTPQKLREYQDIIREVKDANA 144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: ZipA_C] (4)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ZIPA_ECOLI | P77173)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0043093    FtsZ-dependent cytokinesis    A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells.
    GO:0000917    barrier septum assembly    The assembly and arrangement of a septum that spans the plasma membrane interface between progeny cells following cytokinesis. The progeny cells that form a barrier septum are not able to exchange intracellular material.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
cellular component
    GO:0032153    cell division site    The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ZIPA_ECOLI | P77173: 1f46 1f47 1f7w 1f7x 1s1j 1s1s 1y2f

(-) Related Entries Specified in the PDB File

1y2f CRYSTAL STRUCTURE OF ZIPA IN COMPLEX WITH AN INHIBITOR