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(-) Description

Title :  CRYSTAL STRUCTURE OF DOC2B C2A DOMAIN
 
Authors :  M. Giladi, L. Almagor, J. A. Hirsch
Date :  23 Jun 13  (Deposition) - 11 Sep 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  C2, Calcium Binding Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Giladi, L. Michaeli, L. Almagor, D. Bar-On, T. Buki, U. Ashery, D. Khananshvili, J. A. Hirsch
The C2B Domain Is The Primary Ca(2+) Sensor In Doc2B: A Structural And Functional Analysis.
J. Mol. Biol. V. 425 4629 2013
PubMed-ID: 23994332  |  Reference-DOI: 10.1016/J.JMB.2013.08.017

(-) Compounds

Molecule 1 - DOUBLE C2-LIKE DOMAIN-CONTAINING PROTEIN BETA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C2A DOMAIN (UNP RESIDUES 125-255)
    Gene: DOC2B
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: DOC2-BETA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CA2Ligand/IonCALCIUM ION
3FLC1Ligand/IonCITRATE ANION
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CA-1Ligand/IonCALCIUM ION
3FLC-1Ligand/IonCITRATE ANION
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2CA-1Ligand/IonCALCIUM ION
3FLC-1Ligand/IonCITRATE ANION
4SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2CA-1Ligand/IonCALCIUM ION
3FLC-1Ligand/IonCITRATE ANION
4SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2CA-1Ligand/IonCALCIUM ION
3FLC1Ligand/IonCITRATE ANION
4SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:167 , HIS A:169 , ARG A:213 , SER A:215BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARETYR A:165 , LYS A:167 , ARG A:181BINDING SITE FOR RESIDUE BME A 302
3AC3SOFTWARELYS B:167 , HIS B:169 , LYS B:179 , ARG B:213 , HOH B:411 , HOH B:448 , HOH B:460BINDING SITE FOR RESIDUE SO4 B 301
4AC4SOFTWAREASP C:157 , ASP C:163 , ASP C:218 , GLU C:219 , ASP C:220BINDING SITE FOR RESIDUE CA C 301
5AC5SOFTWAREMET C:156 , ASP C:157 , ASP C:218 , ASP C:220 , GLU C:226BINDING SITE FOR RESIDUE CA C 302
6AC6SOFTWARESER B:124 , LYS B:154 , ARG C:209 , LYS C:210 , HOH C:462BINDING SITE FOR RESIDUE SO4 C 303
7AC7SOFTWARETYR D:165 , LYS D:167 , ARG D:181 , ASN D:225BINDING SITE FOR RESIDUE SO4 D 301
8AC8SOFTWAREASN C:159 , ASN C:187 , LYS C:239 , HIS C:242 , LYS C:244 , HOH C:428 , LEU D:135 , ASN D:241 , HIS D:242 , THR D:243 , HOH D:402BINDING SITE FOR RESIDUE FLC D 302

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:249 -B:249
2C:249 -D:249

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu B:171 -Pro B:172
2Leu D:171 -Pro D:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LCV)

(-) 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:123
                                                                                                                                                           
               SCOP domains d4lcva_ A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeehhhheeeeeeeeee.......eeeeeeee...hhh.eee..........eeeeeeee...hhhhhhhheeeeeeee.......eeeeeeeee.hhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcv A 126 ALGTLDFSLLYDQENNALHCTISKAKGLKPLADPYVKLHLLPGASKANKLRTKTLRNTLNPSWNETLTYYGITDEDMIRKTLRISVCDEDKFRHNEFIGETRVPLKKLKPNHTKTFSICLEKQ 253
                                   135       145       155|      170       180       190       200       210       220       230       240       250   
                                                       155|                                                                                            
                                                        161                                                                                            


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains d4lcvb_ B: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee............eeeeeeee...hhh.eee..........eeeeeeeee..hhhhhhhheeeeeeee........eeeeeeee.hhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcv B 124 STALGTLDFSLLYDQENNALHCTISKAKGLKPMDHNGLADPYVKLHLLPGASKANKLRTKTLRNTLNPSWNETLTYYGITDEDMIRKTLRISVCDEDKFRHNEFIGETRVPLKKLKPNHTKTFSICLEKQL 254
                                   133       143       153       163       173       183       193       203       213       223       233       243       253 


Chain C from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains d4lcvc_ C: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhheeeeeeeeee............eeeeeeee...hhh.eee..........eeeeeeee...hhhhhhhheeeeeeee.......eeeeeeeee.hhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcv C 125 TALGTLDFSLLYDQENNALHCTISKAKGLKPMDHNGLADPYVKLHLLPGASKANKLRTKTLRNTLNPSWNETLTYYGITDEDMIRKTLRISVCDEDKFRHNEFIGETRVPLKKLKPNHTKTFSICLEKQ 253
                                   134       144       154       164       174       184       194       204       214       224       234       244         


Chain D from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains d4lcvd_ D: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee.........eeeeeeee...hhh.eee..........eeeeeeeee....hhhhhheeeeeeee.......eeeeeeeee.hhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lcv D 126 ALGTLDFSLLYDQENNALHCTISKAKGLKPMDLADPYVKLHLLPGASKANKLRTKTLRNTLNPSWNETLTYYGITDEDMIRKTLRISVCDEDKFRHNEFIGETRVPLKKLKPNHTKTFSICLEKQL 254
                                   135       145       155 ||    168       178       188       198       208       218       228       238       248      
                                                         157|                                                                                             
                                                          161
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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  4lcv
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 Related Entries

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        DOC2B_RAT | P70610: 4ldc

(-) Related Entries Specified in the PDB File

4ldc CRYSTAL STRUCTURE OF DOC2B C2B DOMAIN