1OMD - JenaLib

Title :   STRUCTURE OF ONCOMODULIN REFINED AT 1.85 ANGSTROMS RESOLUTION. AN EXAMPLE OF EXTENSIVE MOLECULAR AGGREGATION VIA CA2+

Authors :   F. R. Ahmed, M. Przybylska, D. R. Rose, G. I. Birnbaum, M. E. Pippy, J. P. Macmanus

Date :   19 Apr 90 (Deposition) - 15 Jul 91 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Calcium Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. R. Ahmed, M. Przybylska, D. R. Rose, G. I. Birnbaum, M. E. Pippy, J. P. Macmanus
Structure Of Oncomodulin Refined At 1. 85 A Resolution. An Example Of Extensive Molecular Aggregation Via Ca2+.
J. Mol. Biol. V. 216 127 1990
PubMed-ID: 2231727 | Reference-DOI: 10.1016/S0022-2836(05)80065-8
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:90 , ASP A:92 , ASP A:94 , LYS A:96 , GLU A:101 , HOH A:111	BINDING SITE FOR RESIDUE CA A 109
2	AC2	SOFTWARE	ASP A:51 , ASP A:53 , SER A:55 , TYR A:57 , GLU A:62 , HOH A:112	BINDING SITE FOR RESIDUE CA A 110
3	AC3	SOFTWARE	GLN A:54 , GLN A:71 , ASP A:73 , GLU A:79 , HOH A:169 , HOH A:172	BINDING SITE FOR RESIDUE CA A 135
4	CD	AUTHOR	ASP A:51 , ASN A:52 , ASP A:53 , GLN A:54 , SER A:55 , GLY A:56 , TYR A:57 , LEU A:58 , ASP A:59 , GLY A:60 , ASP A:61 , GLU A:62	CALCIUM BINDING SITE 1
5	EF	AUTHOR	ASP A:90 , ASN A:91 , ASP A:92 , GLY A:93 , ASP A:94 , GLY A:95 , LYS A:96 , ILE A:97 , GLY A:98 , ALA A:99 , ASP A:100 , GLU A:101	CALCIUM BINDING SITE 2

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (4, 4)

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000043439	1	ENSRNOE00000008799	chr12:10919773-10919838	66	ONCO_RAT	1-21	21	1	A:2-20	19
1.2	ENSRNOT00000043439	2	ENSRNOE00000008803	chr12:10921087-10921219	133	ONCO_RAT	21-65	45	1	A:20-64	45
1.3	ENSRNOT00000043439	3	ENSRNOE00000008806	chr12:10921665-10921774	110	ONCO_RAT	65-102	38	1	A:64-101	38
1.4	ENSRNOT00000043439	4	ENSRNOE00000336131	chr12:10925315-10925595	281	ONCO_RAT	102-109	8	1	A:101-108	8

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:107
 aligned with ONCO_RAT | P02631 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    12        22        32        42        52        62        72        82        92       102       
             ONCO_RAT     3 ITDILSAEDIAAALQECQDPDTFEPQKFFQTSGLSKMSASQVKDIFRFIDNDQSGYLDGDELKYFLQKFQSDARELTESETKSLMDAADNDGDGKIGADEFQEMVHS 109
               SCOP domains d1omda_ A: Oncomodulin                                                                                      SCOP domains
               CATH domains 1omdA00 A:2-108 EF-hand                                                                                     CATH domains
           Pfam domains (1) ----------------------------------------EF_hand_5-1omdA01 A:42-106                                       -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------efhand-1omdA02 A:81-108      Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhh........hhhhhhhh......hhhhhhhhhhh......eee.hhhh.hhhhh........hhhhhhhhhh.......eeehhhhhhhh.. 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           -------------------------------------------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)
                 1omd A   2 ITDILSAEDIAAALQECQDPDTFEPQKFFQTSGLSKMSASQVKDIFRFIDNDQSGYLDGDELKYFLQKFQSDARELTESETKSLMDAADNDGDGKIGADEFQEMVHS 108
                                    11        21        31        41        51        61        71        81        91       101

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)

CATH Domains (1, 1)

Pfam Domains (2, 2)

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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