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(-) Description

Title :  SAICAR SYNTHETASE (TYPE-1) IN COMPLEX WITH ADP AND AMP
 
Authors :  K. Manjunath, J. Jeyakanthan, K. Sekar
Date :  26 Dec 13  (Deposition) - 31 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Saicar Synthetase-Like Fold, Ligase, Atp Binding, Cair Binding, Aspartate Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Manjunath, J. Jeyakanthan, K. Sekar
Saicar Synthetase (Type-1) In Complex With Adp And Amp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
    Chains: A, B
    EC Number: 6.3.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0239, PURC
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: SAICAR SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 31)

Asymmetric Unit (5, 31)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP3Ligand/IonADENOSINE MONOPHOSPHATE
3BU12Ligand/Ion1,4-BUTANEDIOL
4CD17Ligand/IonCADMIUM ION
5MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP3Ligand/IonADENOSINE MONOPHOSPHATE
3BU12Ligand/Ion1,4-BUTANEDIOL
4CD-1Ligand/IonCADMIUM ION
5MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (4, 42)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AMP9Ligand/IonADENOSINE MONOPHOSPHATE
3BU16Ligand/Ion1,4-BUTANEDIOL
4CD-1Ligand/IonCADMIUM ION
5MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:158 , ASP A:162 , GLU B:158 , ASP B:162BINDING SITE FOR RESIDUE CD A 301
02AC2SOFTWAREHIS A:63 , GLU B:111BINDING SITE FOR RESIDUE CD A 302
03AC3SOFTWAREGLU A:89 , ASP A:128 , AMP A:309BINDING SITE FOR RESIDUE CD A 303
04AC4SOFTWAREASP A:35 , HIS A:127 , HOH A:401BINDING SITE FOR RESIDUE CD A 304
05AC5SOFTWAREGLU A:89 , AMP A:309 , HOH A:463BINDING SITE FOR RESIDUE CD A 306
06AC6SOFTWARELYS A:13 , ASP A:190 , AMP A:308 , CD A:311 , HOH A:438 , HOH A:468BINDING SITE FOR RESIDUE CD A 307
07AC7SOFTWARELYS A:13 , MSE A:15 , HIS A:68 , GLU A:81 , LEU A:83 , MSE A:85 , LYS A:122 , GLU A:177 , ALA A:189 , ASP A:190 , CD A:307 , HOH A:438BINDING SITE FOR RESIDUE AMP A 308
08AC8SOFTWAREGLU A:89 , ARG A:93 , GLY A:98 , SER A:99 , ASP A:173 , LYS A:175 , ASP A:195 , THR A:196 , CYS A:197 , ARG A:198 , ARG A:214 , CD A:303 , CD A:306 , CD A:311 , HOH A:433BINDING SITE FOR RESIDUE AMP A 309
09AC9SOFTWARETYR A:133 , TYR A:134 , LYS A:137 , TYR B:133 , HOH B:453BINDING SITE FOR RESIDUE BU1 A 310
10BC1SOFTWARECD A:307 , AMP A:309 , HOH A:438 , HOH A:468BINDING SITE FOR RESIDUE CD A 311
11BC2SOFTWARECD B:309 , AMP B:312BINDING SITE FOR RESIDUE CD B 301
12BC3SOFTWAREGLU A:111 , HIS B:63BINDING SITE FOR RESIDUE CD B 302
13BC4SOFTWAREGLU B:89 , ASP B:124 , ASP B:128BINDING SITE FOR RESIDUE CD B 303
14BC5SOFTWAREASP B:35 , HIS B:127BINDING SITE FOR RESIDUE CD B 304
15BC6SOFTWAREGLU B:81 , ASP B:181BINDING SITE FOR RESIDUE CD B 305
16BC7SOFTWAREASP A:19 , ASP A:21 , GLU B:125BINDING SITE FOR RESIDUE CD B 306
17BC8SOFTWAREGLU B:226BINDING SITE FOR RESIDUE CD B 307
18BC9SOFTWAREGLU B:89 , AMP B:312 , HOH B:422 , HOH B:423BINDING SITE FOR RESIDUE CD B 308
19CC1SOFTWARELYS B:13 , ASP B:190 , CD B:301 , ADP B:311BINDING SITE FOR RESIDUE CD B 309
20CC2SOFTWARETYR A:133 , TYR B:133 , TYR B:134 , LYS B:137BINDING SITE FOR RESIDUE BU1 B 310
21CC3SOFTWARELYS B:13 , MSE B:15 , HIS B:68 , GLU B:81 , LEU B:83 , MSE B:85 , LYS B:122 , GLU B:177 , ASP B:190 , CD B:309BINDING SITE FOR RESIDUE ADP B 311
22CC4SOFTWAREGLU B:89 , ARG B:93 , GLY B:98 , SER B:99 , ASP B:173 , PHE B:174 , LYS B:175 , THR B:196 , CYS B:197 , ARG B:198 , CD B:301 , CD B:308 , HOH B:422BINDING SITE FOR RESIDUE AMP B 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O81)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O81)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O81)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O81)

(-) Exons   (0, 0)

(no "Exon" information available for 4O81)

(-) 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee..eeee....eeee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeee.hhhhhhh.......eeeeeeeeeee........eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.eee.....eee........eeeee........hhhhhh...hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o81 A  12 AKKmIPIDDDKLImEFKDDATAFDGTKKARFKGKGWLNAQLSVIFFKLLEEHGIKTHFIGVAGGNRLIVEKLDmYPLEVVVRNVVAGSLKKRLPLPEGYELPEPIVELYYKNDELHDPmINYYHAKVLGISLDEIKKIEEIALKVNEILKDYLAKKGIILVDFKLEFGKDKNGDIVLADEISPDTCRFWDAKTKRSLDKDVFRFDKGDLIEAYKEIYERITGEKPEF 238
                               |    21   |    31        41        51        61        71        81   |    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
                               |        25-MSE                                                      85-MSE                                      130-MSE                                                                                                        
                              15-MSE                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....eeeeee..eeee....eeee..hhhhhhhhhhhhhhhhhhhh.....eeee....eeeee..ee..eeeeeeee.hhhhhhh.......eeeeeeeeeee........eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.eee.....eee........eeeee........hhhhhh...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o81 B  12 AKKmIPIDDDKLImEFKDDATAFDGTKKARFKGKGWLNAQLSVIFFKLLEEHGIKTHFIGVAGGNRLIVEKLDmYPLEVVVRNVVAGSLKKRLPLPEGYELPEPIVELYYKNDELHDPmINYYHAKVLGISLDEIKKIEEIALKVNEILKDYLAKKGIILVDFKLEFGKDKNGDIVLADEISPDTCRFWDAKTKRSLDKDVFRFDKGDLIEAYKEIYERITGEKP 236
                               |    21   |    31        41        51        61        71        81   |    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
                              15-MSE    25-MSE                                                      85-MSE                                      130-MSE
   Legend:   → Mismatch (orange background)
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    → 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 4O81)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O81)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O81)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  4o81
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  PUR7_PYRHO | O57978
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  6.3.2.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        PUR7_PYRHO | O57978: 3u54 3u55 4o7l 4o7n 4o7r 4o7s 4o7t 4o7v 4o7w 4o7y 4o7z 4o82 4o83 4o84 4o86

(-) Related Entries Specified in the PDB File

3u54 3u55 4o7l 4o7n 4o7r 4o7s 4o7t 4o7v 4o7w 4o7y 4o7z 4o82 4o83 4o84 4o86