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(-) Description

Title :  CRYSTAL STRUCTURE OF RCL WITH PHOSPHO-TRICIRIBINE
 
Authors :  G. Labesse, A. Padilla, P. A. Kaminski
Date :  04 Jul 12  (Deposition) - 02 Jan 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Deoxyribonucleoside 5'-Monophosphate N-Glycosidase, Hydrolase- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Padilla, C. Amiable, S. Pochet, P. A. Kaminski, G. Labesse
Structure Of The Oncoprotein Rcl Bound To Three Nucleotide Analogues.
Acta Crystallogr. , Sect. D V. 69 247 2013
PubMed-ID: 23385460  |  Reference-DOI: 10.1107/S0907444912045039

(-) Compounds

Molecule 1 - DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE
    Chains: A, B, C, D
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 11-151
    Gene: RCL
    Mutation: YES
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: C-MYC-RESPONSIVE PROTEIN RCL

 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  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2TR54Ligand/Ion5-METHYL-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1,5-DIHYDRO-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-3-AMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2TR52Ligand/Ion5-METHYL-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1,5-DIHYDRO-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-3-AMINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2TR52Ligand/Ion5-METHYL-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1,5-DIHYDRO-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-3-AMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:15 , GLY A:16 , SER A:17 , ILE A:18 , ARG A:19 , GLY A:20 , ILE A:65 , ASN A:69 , SER A:87 , GLY A:89 , GLU A:93 , HOH A:311 , SER B:117 , ALA B:118 , MET B:119BINDING SITE FOR RESIDUE TR5 A 201
2AC2SOFTWARESER A:117 , ALA A:118 , MET A:119 , CYS B:15 , GLY B:16 , SER B:17 , ILE B:18 , ARG B:19 , GLY B:20 , ILE B:65 , ASN B:69 , SER B:87 , GLY B:89 , GLU B:93 , HOH B:318 , HOH B:321BINDING SITE FOR RESIDUE TR5 B 201
3AC3SOFTWAREARG A:37 , SER B:33 , ARG B:36BINDING SITE FOR RESIDUE SO4 B 202
4AC4SOFTWARESER A:33 , ARG A:36 , ARG B:37BINDING SITE FOR RESIDUE SO4 B 203
5AC5SOFTWARECYS C:15 , GLY C:16 , SER C:17 , ILE C:18 , ARG C:19 , GLY C:20 , ASN C:69 , SER C:87 , GLY C:89 , GLU C:93 , HOH C:312 , HOH C:315 , SER D:117 , ALA D:118 , MET D:119BINDING SITE FOR RESIDUE TR5 C 201
6AC6SOFTWAREARG C:37 , SER D:33 , ARG D:36BINDING SITE FOR RESIDUE SO4 C 202
7AC7SOFTWARESER C:117 , ALA C:118 , MET C:119 , CYS D:15 , GLY D:16 , SER D:17 , ILE D:18 , ARG D:19 , GLY D:20 , HIS D:45 , VAL D:46 , ILE D:65 , ASN D:69 , SER D:87 , GLY D:89 , GLU D:93 , HOH D:311BINDING SITE FOR RESIDUE TR5 D 201
8AC8SOFTWARESER C:33 , ARG C:36 , ARG D:37BINDING SITE FOR RESIDUE SO4 D 202
9AC9SOFTWARESER D:33 , HOH D:317BINDING SITE FOR RESIDUE SO4 D 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FYH)

(-) 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:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeeeehhhhh...hhhhhh......eeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyh A   9 RRSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAY 150
                                    18        28        38     || 63        73        83        93       103       113       123       133       143       
                                                              44|                                                                                          
                                                               60                                                                                          


Chain B from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhh......eeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyh B   9 RRSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAY 150
                                    18        28        38    ||  65        75        85        95       105       115       125       135       145     
                                                             43|                                                                                         
                                                              61                                                                                         


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhh......eeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fyh C   9 RRSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAY 150
                                    18        28        38    ||  65        75        85        95       105       115       125       135       145     
                                                             43|                                                                                         
                                                              61                                                                                         


Chain D from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhh...ee.hhhhhh.hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhh......eeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fyh D   9 RRSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADAGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAY 150
                                    18        28        38        48|       68        78        88        98       108       118       128       138       148  
                                                                  48|                                                                                           
                                                                   59
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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        DNPH1_RAT | O35820: 2khz 2klh 4fyi 4fyk 4kxl 4kxm 4kxn 4p5d

(-) Related Entries Specified in the PDB File

2klh 4fyi 4fyk