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(-) Description

Title :  LCD1 GAF DOMAIN IN COMPLEX WITH CAMP LIGAND
 
Authors :  C. R. Guzzo, N. K. Maciel, A. S. Barbosa, C. S. Farah
Date :  01 Jun 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Gaf Domain, Camp Binding Domain, Effector Domain, Regulates The Dgc Activity Of The Ggdef Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. N. Da Costa Vasconcelos, N. K. Maciel, D. C. Favaro, L. C. De Oliveira, A. S. Barbosa, R. K. Salinas, R. F. De Souza, C. S. Farah, C. R. Guzzo
Structural And Enzymatic Characterization Of A Camp-Dependent Diguanylate Cyclase From Pathogenic Leptospira Species.
J. Mol. Biol. 2017
PubMed-ID: 28601495  |  Reference-DOI: 10.1016/J.JMB.2017.06.002

(-) Compounds

Molecule 1 - CGMP-SPECIFIC PHOSPHODIESTERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RP
    Expression System Taxid: 562
    Gene: LIC_13137
    Organism Scientific: LEPTOSPIRA INTERROGANS SEROGROUP ICTEROHAEMORRHAGIAE SEROVAR COPENHAGENI (STRAIN FIOCRUZ L1-130)
    Organism Taxid: 267671
    Strain: FIOCRUZ L1-130

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:46 , TRP A:47 , SER A:48 , GLU A:65 , ILE A:67 , GLY A:82 , ILE A:83 , ALA A:84 , PHE A:105 , SER A:106 , VAL A:109 , ASP A:110 , PHE A:115 , THR A:117 , ILE A:120 , GLU A:136 , HOH A:304 , HOH A:314binding site for residue CMP A 201
2AC2SOFTWAREASN B:46 , TRP B:47 , SER B:48 , GLU B:65 , ILE B:67 , GLY B:82 , ILE B:83 , ALA B:84 , PHE B:105 , SER B:106 , VAL B:109 , ASP B:110 , PHE B:115 , THR B:117 , ILE B:120 , GLU B:136 , HOH B:332binding site for residue CMP B 201
3AC3SOFTWAREASN C:46 , TRP C:47 , SER C:48 , GLU C:65 , ILE C:67 , GLY C:82 , ILE C:83 , ALA C:84 , PHE C:105 , SER C:106 , VAL C:109 , ASP C:110 , PHE C:115 , THR C:117 , ILE C:120 , GLU C:136 , HOH C:322binding site for residue CMP C 201
4AC4SOFTWAREASN D:46 , TRP D:47 , SER D:48 , GLU D:65 , ILE D:67 , GLY D:82 , ILE D:83 , ALA D:84 , PHE D:105 , SER D:106 , VAL D:109 , ASP D:110 , PHE D:115 , THR D:117 , ILE D:120 , GLU D:136 , HOH D:319 , HOH D:338binding site for residue CMP D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5W10)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5W10)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5W10)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5W10)

(-) Exons   (0, 0)

(no "Exon" information available for 5W10)

(-) 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:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee..hhhhhh...ee..hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5w10 A   3 LKDSKPELIKLYSSLGKIITSSLEQQEVLSAVmEEVRLFFSPKNWSLmRYDENSEELFFLIAEGIQFNHIRSIRLKSGEGIAGSVVQTKSPIFVENVKNDPRFSKKVDEKTGFETKTIIAVPmIFRGEVHGVIELVNRFDGSSFSPEDLVILQTIADFTAISLAHSDQYEKTK 175
                                    12        22        32  |     42       |52        62        72        82        92       102       112       122  |    132       142       152       162       172   
                                                           35-MSE         50-MSE                                                                    125-MSE                                              


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee..hhhhhh...ee..hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5w10 B   4 KDSKPELIKLYSSLGKIITSSLEQQEVLSAVmEEVRLFFSPKNWSLmRYDENSEELFFLIAEGIQFNHIRSIRLKSGEGIAGSVVQTKSPIFVENVKNDPRFSKKVDEKTGFETKTIIAVPmIFRGEVHGVIELVNRFDGSSFSPEDLVILQTIADFTAISLAHSDQYEKTK 175
                                    13        23        33 |      43      | 53        63        73        83        93       103       113       123 |     133       143       153       163       173  
                                                          35-MSE         50-MSE                                                                    125-MSE                                              


Chain C from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee..hhhhhh...ee..hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5w10 C   1 mTLKDSKPELIKLYSSLGKIITSSLEQQEVLSAVmEEVRLFFSPKNWSLmRYDENSEELFFLIAEGIQFNHIRSIRLKSGEGIAGSVVQTKSPIFVENVKNDPRFSKKVDEKTGFETKTIIAVPmIFRGEVHGVIELVNRFSFSPEDLVILQTIADFTAISLAHSDQYEKT 174
                            |       10        20        30    |   40        50        60        70        80        90       100       110       120    |  130       140||     153       163       173 
                            1-MSE                            35-MSE         50-MSE                                                                    125-MSE         141|                             
                                                                                                                                                                       145                             


Chain D from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee..hhhhhh...ee..hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5w10 D   1 mTLKDSKPELIKLYSSLGKIITSSLEQQEVLSAVmEEVRLFFSPKNWSLmRYDENSEELFFLIAEGIQFNHIRSIRLKSGEGIAGSVVQTKSPIFVENVKNDPRFSKKVDEKTGFETKTIIAVPmIFRGEVHGVIELVNRSFSPEDLVILQTIADFTAISLAHSDQYEKT 174
                            |       10        20        30    |   40        50        60        70        80        90       100       110       120    |  130       140|      154       164       174
                            1-MSE                            35-MSE         50-MSE                                                                    125-MSE        140|                             
                                                                                                                                                                      145
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  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 5W10)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5W10)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5W10)

(-) Gene Ontology  (0, 0)

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