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(-) Description

Title :  REFINEMENT OF RECOMBINANT ONCOMODULIN AT 1.30 ANGSTROMS RESOLUTION
 
Authors :  F. R. Ahmed, D. R. Rose, S. V. Evans, M. E. Pippy, R. To
Date :  27 Aug 92  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. R. Ahmed, D. R. Rose, S. V. Evans, M. E. Pippy, R. To
Refinement Of Recombinant Oncomodulin At 1. 30 A Resolution.
J. Mol. Biol. V. 230 1216 1993
PubMed-ID: 8487302  |  Reference-DOI: 10.1006/JMBI.1993.1237
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAT ONCOMODULIN
    Chains: A
    Engineered: YES
    Organ: LIVER
    Organism Common: BLACK RAT
    Organism Scientific: RATTUS RATTUS
    Organism Taxid: 10117

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:90 , ASP A:92 , ASP A:94 , LYS A:96 , GLU A:101 , HOH A:111BINDING SITE FOR RESIDUE CA A 109
2AC2SOFTWAREASP A:51 , ASP A:53 , SER A:55 , TYR A:57 , GLU A:62 , HOH A:112BINDING SITE FOR RESIDUE CA A 110
3AC3SOFTWARELYS A:37 , HOH A:125 , HOH A:163 , HOH A:174 , HOH A:180 , HOH A:181 , HOH A:200BINDING SITE FOR RESIDUE CA A 124
4AC4SOFTWAREGLN A:54 , GLN A:71 , ASP A:73 , GLU A:79 , HOH A:127 , HOH A:129BINDING SITE FOR RESIDUE CA A 135

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RRO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.ONCO_RAT39-74
78-109		  2A:38-73
A:77-108
2EF_HAND_1PS00018 EF-hand calcium-binding domain.ONCO_RAT52-64
91-103		  2A:51-63
A:90-102

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000434391ENSRNOE00000008799chr12:10919773-1091983866ONCO_RAT1-21211A:1-2020
1.2ENSRNOT000000434392ENSRNOE00000008803chr12:10921087-10921219133ONCO_RAT21-65451A:20-6445
1.3ENSRNOT000000434393ENSRNOE00000008806chr12:10921665-10921774110ONCO_RAT65-102381A:64-10138
1.4ENSRNOT000000434394ENSRNOE00000336131chr12:10925315-10925595281ONCO_RAT102-10981A:101-1088

(-) 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:108
 aligned with ONCO_RAT | P02631 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:108
                                    11        21        31        41        51        61        71        81        91       101        
             ONCO_RAT     2 SITDILSAEDIAAALQECQDPDTFEPQKFFQTSGLSKMSASQVKDIFRFIDNDQSGYLDGDELKYFLQKFQSDARELTESETKSLMDAADNDGDGKIGADEFQEMVHS 109
               SCOP domains d1rroa_ A: Oncomodulin                                                                                       SCOP domains
               CATH domains 1rroA00 A:1-108 EF-hand                                                                                      CATH domains
           Pfam domains (1) -----------------------------------------EF_hand_5-1rroA01 A:42-106                                       -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------efhand-1rroA02 A:81-107    - Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhh........hhhhhhhh......hhhhhhhhhhh......ee..hhhhhhhhhh........hhhhhhhhhh........eehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------------------EF_HAND_2  PDB: A:38-73             ---EF_HAND_2  PDB: A:77-108         PROSITE (1)
                PROSITE (2) --------------------------------------------------EF_HAND_1    --------------------------EF_HAND_1    ------ PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:1-2-------------------------------------------Exon 1.3  PDB: A:64-101               ------- Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: A:20-64 UniProt: 21-65        ------------------------------------Exon 1.4 Transcript 1 (2)
                 1rro A   1 SITDILSAEDIAAALQECQDPDTFEPQKFFQTSGLSKMSASQVKDIFRFIDNDQSGYLDGDELKYFLQKFQSDARELTESETKSLMDAADNDGDGKIGADEFQEMVHS 108
                                    10        20        30        40        50        60        70        80        90       100
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ONCO_RAT | P02631)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0051480    regulation of cytosolic calcium ion concentration    Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ONCO_RAT | P02631: 1omd 2nln

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RRO)