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(-) Description

Title :  LYS6-LINKED DI-UBIQUITIN
 
Authors :  S. Gao, M. Pan, Y. Zheng, L. Liu
Date :  26 Jul 16  (Deposition) - 02 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (1x)
Keywords :  Polyubiquitin Chains, Quasi-Racemic Crystal, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Gao, M. Pan, Y. Zheng, Y. Huang, Q. Zheng, D. Sun, L. Lu, X. Tan, X. Tan, H. Lan, J. Wang, T. Wang, J. Wang, L. Liu
Monomer/Oligomer Quasi-Racemic Protein Crystallography
J. Am. Chem. Soc. V. 138 14497 2016
PubMed-ID: 27768314  |  Reference-DOI: 10.1021/JACS.6B09545

(-) Compounds

Molecule 1 - UBIQUITIN
    Chains: A
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 2 - D-UBIQUITIN
    Chains: B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (17, 70)

Asymmetric Unit (17, 70)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2DAR4Mod. Amino AcidD-ARGININE
3DAS5Mod. Amino AcidD-ASPARTIC ACID
4DGL6Mod. Amino AcidD-GLUTAMIC ACID
5DGN6Mod. Amino AcidD-GLUTAMINE
6DHI1Mod. Amino AcidD-HISTIDINE
7DIL7Mod. Amino AcidD-ISOLEUCINE
8DLE9Mod. Amino AcidD-LEUCINE
9DLY7Mod. Amino AcidD-LYSINE
10DNE1Mod. Amino AcidD-NORLEUCINE
11DPN2Mod. Amino AcidD-PHENYLALANINE
12DPR3Mod. Amino AcidD-PROLINE
13DSG2Mod. Amino AcidD-ASPARAGINE
14DSN3Mod. Amino AcidD-SERINE
15DTH7Mod. Amino AcidD-THREONINE
16DTY1Mod. Amino AcidD-TYROSINE
17DVA4Mod. Amino AcidD-VALINE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DAL-1Mod. Amino AcidD-ALANINE
2DAR-1Mod. Amino AcidD-ARGININE
3DAS-1Mod. Amino AcidD-ASPARTIC ACID
4DGL-1Mod. Amino AcidD-GLUTAMIC ACID
5DGN-1Mod. Amino AcidD-GLUTAMINE
6DHI-1Mod. Amino AcidD-HISTIDINE
7DIL-1Mod. Amino AcidD-ISOLEUCINE
8DLE-1Mod. Amino AcidD-LEUCINE
9DLY-1Mod. Amino AcidD-LYSINE
10DNE-1Mod. Amino AcidD-NORLEUCINE
11DPN-1Mod. Amino AcidD-PHENYLALANINE
12DPR-1Mod. Amino AcidD-PROLINE
13DSG-1Mod. Amino AcidD-ASPARAGINE
14DSN-1Mod. Amino AcidD-SERINE
15DTH-1Mod. Amino AcidD-THREONINE
16DTY-1Mod. Amino AcidD-TYROSINE
17DVA-1Mod. Amino AcidD-VALINE
Biological Unit 2 (17, 70)
No.NameCountTypeFull Name
1DAL2Mod. Amino AcidD-ALANINE
2DAR4Mod. Amino AcidD-ARGININE
3DAS5Mod. Amino AcidD-ASPARTIC ACID
4DGL6Mod. Amino AcidD-GLUTAMIC ACID
5DGN6Mod. Amino AcidD-GLUTAMINE
6DHI1Mod. Amino AcidD-HISTIDINE
7DIL7Mod. Amino AcidD-ISOLEUCINE
8DLE9Mod. Amino AcidD-LEUCINE
9DLY7Mod. Amino AcidD-LYSINE
10DNE1Mod. Amino AcidD-NORLEUCINE
11DPN2Mod. Amino AcidD-PHENYLALANINE
12DPR3Mod. Amino AcidD-PROLINE
13DSG2Mod. Amino AcidD-ASPARAGINE
14DSN3Mod. Amino AcidD-SERINE
15DTH7Mod. Amino AcidD-THREONINE
16DTY1Mod. Amino AcidD-TYROSINE
17DVA4Mod. Amino AcidD-VALINE

(-) Sites  (0, 0)

(no "Site" information available for 5GOB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GOB)

(-) 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:76
                                                                                                           
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  5gob A  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76
                                    10        20        30        40        50        60        70      


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                         
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  5gob B  1 xxxxxxxxxGxxxxxxxxxxxxxxxxxxxxxxxxGxxxxxxxxxxxGxxxxxGxxxxxxxxxxxxxxxxxxxxx 74
                            ||||||||10||||||||20||||||||30|||| |||40|||||| |50|| |||||60||||||||70||||
                            1-DNE|||| 12-DTH|||21-DAS|||30-DIL |||40-DGN|| |50-DLE||||60-DSG|||69-DLE|
                             2-DGN||| |13-DIL|||22-DTH|||31-DGN||||41-DGN| ||51-DGL||||61-DIL|||70-DVA
                              3-DIL|| | 14-DTH|| 23-DIL|| 32-DAS||| 42-DAR || 52-DAS||| 62-DGN|| 71-DLE
                               4-DPN| |  15-DLE|  24-DGL|  33-DLY||  43-DLE||   54-DAR|  63-DLY|  72-DAR
                                5-DVA |   16-DGL   25-DSG   34-DGL|   44-DIL|    55-DTH   64-DGL   73-DLE
                                 6-DLY|    17-DVA   26-DVA    36-DIL   45-DPN     56-DLE   65-DSN   74-DAR
                                  7-DTH     18-DGL   27-DLY    37-DPR   46-DAL     57-DSN   66-DTH    
                                   8-DLE     19-DPR   28-DAL    38-DPR    48-DLY    58-DAS   67-DLE   
                                    9-DTH     20-DSN   29-DLY    39-DAS    49-DGN    59-DTY   68-DHI
   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 5GOB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (103, 181)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RL40_HUMAN | P62987: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2lj5 2mbh 2mjb 2mur 2n3u 2n3v 2n3w 2nbd 2nbe 2nr2 2o6v 2ojr 2pe9 2pea 2rsu 2w9n 2wdt 2xew 2xk5 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3phd 4hjk 4jio 4p4h 4pig 4pih 4pij 4rf0 4rf1 4s1z 4ug0 4v6x 4xkl 5aj0 5go7 5go8 5goc 5god 5gog 5goh 5goi 5goj 5gok 5hpk 5hpl 5hps 5hpt 5j26 5j8p 5jbv 5jby 5t2c
        UBB_HUMAN | P0CG47: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2mbb 2mro 2msg 2n13 2nr2 2o6v 2ojr 2pe9 2pea 2w9n 2wdt 2xew 2xk5 2y5b 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3oj3 3oj4 3ons 3phd 3ptf 3zlz 3znh 4uel 4uf6 4whv 4wlr 4wur 4wzp 4xof 4zfr 4zft 4zpz 4zux 5bnb 5caw 5cra 5cvm 5cvn 5cvo 5d0k 5d0m 5dfl 5dk8 5e6j 5edv 5emz 5eya 5gjq 5go7 5go8 5goc 5god 5gog 5goh 5goi 5goj 5gok 5ibk 5ifr 5j8p 5jbv 5jby 5jg6 5jp3 5jtj 5jtv 5k9p 5kgf 5khy 5l8h 5l8w 5l9t 5ln1 5lrv 5lrw 5lrx 5m93 5mnj 5n2w 5n38 5nl5 5nlj 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1y 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5

(-) Related Entries Specified in the PDB File

5go7 5go8 5goc 5god 5gog 5goh 5goi 5goj 5gok