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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN RELATED TO DAN AND CERBERUS (PRDC)
 
Authors :  X. Deng, K. T. Nolan, C. Kattamuri, T. B. Thompson
Date :  19 Mar 13  (Deposition) - 24 Jul 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cystine Knot, Dan Domain, Can Domain, Bmp Antagonist, Bmp-2, Bmp-4, Bmp-7, Gdf-5, Gsh, Extracellular, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nolan, C. Kattamuri, D. M. Luedeke, X. Deng, A. Jagpal, F. Zhang, R. J. Linhardt, A. P. Kenny, A. M. Zorn, T. B. Thompson
Structure Of Protein Related To Dan And Cerberus: Insights Into The Mechanism Of Bone Morphogenetic Protein Antagonism
Structure V. 21 1417 2013
PubMed-ID: 23850456  |  Reference-DOI: 10.1016/J.STR.2013.06.005

(-) Compounds

Molecule 1 - GREMLIN-2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 22-168
    Gene: GREM2, CKTSF1B2, PRDC
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: CYSTEINE KNOT SUPERFAMILY 1, BMP ANTAGONIST 2, PROTEIN RELATED TO DAN AND CERBERUS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2GOL12Ligand/IonGLYCEROL
3GSH4Ligand/IonGLUTATHIONE
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GOL8Ligand/IonGLYCEROL
3GSH2Ligand/IonGLUTATHIONE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GOL4Ligand/IonGLYCEROL
3GSH2Ligand/IonGLUTATHIONE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:58 , ARG B:79BINDING SITE FOR RESIDUE GOL A 201
02AC2SOFTWAREILE A:49BINDING SITE FOR RESIDUE GOL A 202
03AC3SOFTWAREARG A:108 , HIS A:109 , LYS A:111 , ASP A:115BINDING SITE FOR RESIDUE GOL A 203
04AC4SOFTWARECYS A:157 , MET A:158BINDING SITE FOR RESIDUE GOL A 204
05AC5SOFTWAREGLU A:84 , ARG A:145 , SER B:89BINDING SITE FOR RESIDUE GOL A 205
06AC6SOFTWARETYR A:105 , GLN A:118 , CYS A:120 , VAL A:160 , PHE B:122 , LYS B:124 , PRO B:125 , GSH B:205BINDING SITE FOR RESIDUE GSH A 206
07AC7SOFTWAREARG B:95 , ARG B:127 , LYS B:153 , ARG D:90 , ILE D:132 , HOH D:301 , HOH D:304 , HOH D:310BINDING SITE FOR RESIDUE CIT B 201
08AC8SOFTWAREHIS B:154 , THR D:129 , SER D:130BINDING SITE FOR RESIDUE GOL B 202
09AC9SOFTWAREGLU B:64 , GLN B:118BINDING SITE FOR RESIDUE GOL B 203
10BC1SOFTWAREPHE B:144BINDING SITE FOR RESIDUE GOL B 204
11BC2SOFTWAREPHE A:122 , LYS A:124 , GSH A:206 , GLN B:118 , CYS B:120BINDING SITE FOR RESIDUE GSH B 205
12BC3SOFTWAREHIS C:154 , ARG C:156 , HOH C:312BINDING SITE FOR RESIDUE GOL C 201
13BC4SOFTWAREARG C:95 , LYS C:153BINDING SITE FOR RESIDUE GOL C 202
14BC5SOFTWAREGLU B:85 , GLY B:86 , ARG C:79 , LEU C:93 , HOH C:302BINDING SITE FOR RESIDUE GOL C 203
15BC6SOFTWAREGLN C:118 , CYS C:120BINDING SITE FOR RESIDUE GSH C 204
16BC7SOFTWAREGLN B:126 , ARG B:127 , ARG B:156 , LYS D:151 , LYS D:153BINDING SITE FOR RESIDUE CIT D 201
17BC8SOFTWAREARG B:79 , THR B:91 , PRO D:142 , PHE D:144BINDING SITE FOR RESIDUE GOL D 202
18BC9SOFTWAREPHE C:122 , GLN D:118 , CYS D:120BINDING SITE FOR RESIDUE GSH D 203

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:73 -A:123
2A:87 -A:137
3A:97 -A:155
4A:101 -A:157
5B:73 -B:123
6B:87 -B:137
7B:97 -B:155
8B:101 -B:157
9C:73 -C:123
10C:87 -C:137
11C:97 -C:155
12C:101 -C:157
13D:73 -D:123
14D:87 -D:137
15D:97 -D:155
16D:101 -D:157

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:141 -Pro A:142
2Lys B:111 -Lys B:112
3Asp B:141 -Pro B:142
4Asp C:141 -Pro C:142
5Asp D:141 -Pro D:142
6Pro D:142 -Pro D:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JPH)

(-) 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:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.......eeeeeeeeeeeeeeeeee........eeeee.eeeeeeeeeeeeeee.......eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4jph A  46 HHQIKEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSV 160
                                    55        65        75        85        95       105       115       125       135       145       155     


Chain B from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeeeeeeeee..........eeee.eeeeeeeeeeeeeee.......eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4jph B  50 KEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSV 160
                                    59        69        79        89        99       109       119       129       139       149       159 


Chain C from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eeeeeeeeeee.......eeeeeeeeeeeeeeeee..........eeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4jph C  60 LVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSV 160
                                    69        79        89        99       109       119       129       139       149       159 


Chain D from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeeeeeeeeee........eeeeeeeeeeeeeeeeeeee.........eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4jph D  50 KEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSV 160
                                    59        69        79        89        99       109       119       129       139       149       159
   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  (0, 0)

(no "SCOP Domain" information available for 4JPH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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        GREM2_MOUSE | O88273: 5hk5

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