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(-) Description

Title :  DCNL COMPLEX WITH N-TERMINALLY ACETYLATED NEDD8 E2 PEPTIDE
 
Authors :  J. K. Monda, D. C. Scott, D. J. Miller, J. W. Harper, E. J. Bennett, B. A. Sc
Date :  25 Jul 12  (Deposition) - 28 Nov 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.28
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  E3 Ligase, Ligase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Monda, D. C. Scott, D. J. Miller, J. Lydeard, D. King, J. W. Harper, E. J. Bennett, B. A. Schulman
Structural Conservation Of Distinctive N-Terminal Acetylation-Dependent Interactions Across A Family Of Mammalian Nedd8 Ligation Enzymes.
Structure V. 21 42 2013
PubMed-ID: 23201271  |  Reference-DOI: 10.1016/J.STR.2012.10.013

(-) Compounds

Molecule 1 - DCN1-LIKE PROTEIN 2
    Chains: A, B, D, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DCUN1D2, C13ORF17, DCUN1L2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DCUN1 DOMAIN-CONTAINING PROTEIN 2, DEFECTIVE IN CULLIN NEDDYLATION PROTEIN 1-LIKE PROTEIN 2
 
Molecule 2 - NEDD8-CONJUGATING ENZYME UBC12
    Chains: C, E, F, H
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A    F  
Biological Unit 2 (1x):  BC     
Biological Unit 3 (1x):    DE   
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1AME4Mod. Amino AcidN-ACETYLMETHIONINE
2BR2Ligand/IonBROMIDE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AME1Mod. Amino AcidN-ACETYLMETHIONINE
2BR-1Ligand/IonBROMIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AME1Mod. Amino AcidN-ACETYLMETHIONINE
2BR-1Ligand/IonBROMIDE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1AME1Mod. Amino AcidN-ACETYLMETHIONINE
2BR-1Ligand/IonBROMIDE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1AME1Mod. Amino AcidN-ACETYLMETHIONINE
2BR-1Ligand/IonBROMIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:118 , LYS A:120 , SER G:118 , LYS G:120BINDING SITE FOR RESIDUE BR A 301
2AC2SOFTWARESER B:118 , SER D:118BINDING SITE FOR RESIDUE BR B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GAO)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.ee..eeeeehhhhhhhhhhhh.....hhhhhhhhhhhh......eehhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh.....hhhhhhhhhhhh...eehhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gao A  60 GSKKKLERLYGRYKDPQDENKIGVDGIQQFCDDLSLDPASISVLVIAWKFRAATQCEFSRKEFLDGMTELGCDSMEKLKALLPRLEQELKDTAKFKDFYQFTFTFAKNPGQKGLDLEMAVAYWKLVLSGRFKFLDLWNTFLMEHHKRSIPRDTWNLLLDFGNMIADDMSNYDEEGAWPVLIDDFVEYARPVVT 252
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh........eehhhhhhhhhhhhh....hhhhhhhhhhhh......eehhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gao B  60 GSKKKLERLYGRYKDPQDENKIGVDGIQQFCDDLSLDPASISVLVIAWKFRAATQCEFSRKEFLDGMTELGCDSMEKLKALLPRLEQELKDTAKFKDFYQFTFTFAKNPGQKGLDLEMAVAYWKLVLSGRFKFLDLWNTFLMEHHKRSIPRDTWNLLLDFGNMIADDMSNYDEEGAWPVLIDDFVEYARPVV 251
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249  


Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4gao C   1 xIKLFSLKQQ  10
                            |       10
                            1-AME     


Chain D from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh........eehhhhhhhhhhhh.....hhhhhhhhhhhh......eehhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh.....hhhhhhhhhhhh...eehhhhhhhhhhhhhhh.............hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gao D  62 KKKLERLYGRYKDPQDENKIGVDGIQQFCDDLSLDPASISVLVIAWKFRAATQCEFSRKEFLDGMTELGCDSMEKLKALLPRLEQELKDTAKFKDFYQFTFTFAKNPGQKGLDLEMAVAYWKLVLSGRFKFLDLWNTFLMEHHKRSIPRDTWNLLLDFGNMIADDMSNYDEEGAWPVLIDDFVEYARP 249
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        


Chain E from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4gao E   1 xIKLFSLKQQ  10
                            |       10
                            1-AME     


Chain F from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4gao F   1 xIKLFSLKQQK  11
                            |       10 
                            1-AME      


Chain G from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhee..eeeeehhhhhhhhhhhh.....hhhhhhhhhhhh......eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gao G  60 GSKKKLERLYGRYKDPQDENKIGVDGIQQFCDDLSLDPASISVLVIAWKFRAATQCEFSRKEFLDGMTELGCDSMEKLKALLPRLEQELKDTAKFKDFYQFTFTFAKNPGQKGLDLEMAVAYWKLVLSGRFKFLDLWNTFLMEHHKRSIPRDTWNLLLDFGNMIADDMSNYDEEGAWPVLIDDFVEYARPVVT 252
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249   


Chain H from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4gao H   1 xIKLFSLKQQ  10
                            |       10
                            1-AME
   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 4GAO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 24)

Asymmetric Unit(hide GO term definitions)

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        UBC12_HUMAN | P61081: 1tt5 1y8x 2nvu 3tdu 3tdz 4p5o

(-) Related Entries Specified in the PDB File

4gba