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(-) Description

Title :  CRYSTAL STRUCTURE OF ZN2.3-HUB (HUMAN UBIQUITIN) ADDUCT FROM A SOLUTION 70 MM ZINC ACETATE/1.3 MM HUB
 
Authors :  S. Fermani, G. Falini, M. Calvaresi, A. Bottoni, F. Arnesano, G. Natile
Date :  17 Apr 13  (Deposition) - 08 May 13  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ligase, Zn Adduct (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fermani, G. Falini, M. Calvaresi, A. Bottoni, V. Calo, V. Mangini, F. Arnesano, G. Natile
Conformational Selection Of Ubiquitin Quaternary Structures Driven By Zinc Ions.
Chemistry V. 19 15480 2013
PubMed-ID: 24123543  |  Reference-DOI: 10.1002/CHEM.201302229
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN
    Chains: A, B, C
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-76
    Gene: UBC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLYUBIQUITIN-C

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4ZN9Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:1 , GLU A:16 , GLU B:51 , HOH C:201BINDING SITE FOR RESIDUE ZN A 101
02AC2SOFTWAREGLU A:18 , ZN A:104 , ASP C:21 , EDO C:104 , HOH C:254BINDING SITE FOR RESIDUE ZN A 102
03AC3SOFTWAREASP A:21 , ZN A:104 , EDO A:106 , HOH A:241 , GLU B:18BINDING SITE FOR RESIDUE ZN A 103
04AC4SOFTWAREGLU A:18 , ZN A:102 , ZN A:103 , HOH A:241 , GLU B:18 , GLU C:18 , ZN C:102 , HOH C:233 , HOH C:254 , HOH C:271BINDING SITE FOR RESIDUE ZN A 104
05AC5SOFTWARETHR A:14 , LYS A:33 , HOH B:248BINDING SITE FOR RESIDUE ACT A 105
06AC6SOFTWAREGLU A:16 , GLU A:18 , ASP A:21 , LYS A:29 , ZN A:103 , GLU B:18BINDING SITE FOR RESIDUE EDO A 106
07AC7SOFTWAREASP A:58 , HOH A:260 , HOH A:280 , LEU B:15 , GLU B:16 , LYS B:29 , ACT C:103BINDING SITE FOR RESIDUE EDO A 107
08AC8SOFTWAREPRO A:37 , ASP A:39 , HOH A:283 , ALA C:46 , HIS C:68 , HOH C:217 , HOH C:258BINDING SITE FOR RESIDUE PEG A 108
09AC9SOFTWAREHIS A:68 , LYS B:6 , HIS B:68 , ACT B:104 , HOH B:256BINDING SITE FOR RESIDUE ZN B 101
10BC1SOFTWAREHOH A:244 , MET B:1 , GLU B:16 , ZN B:103 , GLU C:51BINDING SITE FOR RESIDUE ZN B 102
11BC2SOFTWAREASP A:32 , HOH A:244 , ZN B:102 , GLU C:51 , HOH C:242BINDING SITE FOR RESIDUE ZN B 103
12BC3SOFTWARELYS A:6 , THR A:66 , HIS A:68 , LYS B:6 , HIS B:68 , ZN B:101 , HOH B:256 , HOH B:277BINDING SITE FOR RESIDUE ACT B 104
13BC4SOFTWARELYS A:63 , LYS B:48 , GLN B:49 , GLN C:31 , ASP C:32 , HOH C:218BINDING SITE FOR RESIDUE EDO B 105
14BC5SOFTWAREGLU A:51 , MET C:1 , GLU C:16 , HOH C:222BINDING SITE FOR RESIDUE ZN C 101
15BC6SOFTWAREZN A:104 , ASP B:21 , GLU C:18 , ACT C:103 , HOH C:233BINDING SITE FOR RESIDUE ZN C 102
16BC7SOFTWAREEDO A:107 , GLU B:16 , GLU B:18 , ASP B:21 , LYS B:29 , HOH B:265 , GLU C:18 , ZN C:102 , HOH C:271BINDING SITE FOR RESIDUE ACT C 103
17BC8SOFTWAREGLU A:18 , ZN A:102 , GLU C:18 , ASP C:21 , LYS C:29 , HOH C:270 , HOH C:271BINDING SITE FOR RESIDUE EDO C 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K7U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K7U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K7U)

(-) Exons   (0, 0)

(no "Exon" information available for 4K7U)

(-) 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:72
                                                                                                       
               SCOP domains d4k7ua_ A: Ubiquitin                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhh.eee..ee......hhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  4k7u A  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
                                    10        20        30        40        50        60        70  


Chain B from PDB  Type:PROTEIN  Length:72
                                                                                                       
               SCOP domains d4k7ub_ B: Ubiquitin                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  4k7u B  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
                                    10        20        30        40        50        60        70  


Chain C from PDB  Type:PROTEIN  Length:72
                                                                                                       
               SCOP domains d4k7uc_ C: Ubiquitin                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  4k7u C  1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
                                    10        20        30        40        50        60        70
   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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K7U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K7U)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBC_HUMAN | P0CG48: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1ogw 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1xqq 1yx5 1yx6 1zgu 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2gmi 2hth 2ibi 2j7q 2jf5 2jri 2jy6 2jzz 2k25 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2kx0 2l0f 2l0t 2l3z 2ld9 2lvo 2lvp 2lvq 2lz6 2mbo 2mbq 2mcn 2mi8 2mj5 2mor 2mre 2mws 2n2k 2nr2 2o6v 2ojr 2pe9 2pea 2rr9 2rsu 2ru6 2w9n 2wdt 2xew 2xk5 2y5b 2z59 2zcb 2zvn 2zvo 3a33 3alb 3aul 3b08 3b0a 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9o 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3ofi 3oj3 3oj4 3ons 3phd 3prm 3pt2 3ptf 3q3f 3rul 3tmp 3u30 3ugb 3v6c 3v6e 3vfk 3vuw 3vux 3vuy 3wxe 3wxf 3zlz 3znh 3zni 3znz 4ap4 4auq 4bos 4boz 4bvu 4ddg 4ddi 4dhj 4dhz 4fjv 4hk2 4hxd 4i6l 4i6n 4ig7 4ium 4jqw 4k1r 4k7s 4k7w 4ksk 4ksl 4lcd 4ldt 4mdk 4mm3 4msm 4msq 4nqk 4un2 4v3k 4v3l 4wzp 4xok 4xol 4zqs 5a5b 5af4 5af5 5af6 5ait 5aiu 5b83 5c7j 5c7m 5e6j 5h07 5nl4 5nlf 5nli 5nmc

(-) Related Entries Specified in the PDB File

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3ehv X-RAY STRUCTURE OF HUMAN UBIQUITIN ZN(II) ADDUCT
3n30 CRYSTAL STRUCTURE OF CUBIC ZN3-HUB (HUMAN UBIQUITIN) ADDUCT
3n32 THE CRYSTAL STRUCTURE OF HUMAN UBIQUITIN ADDUCT WITH ZEISE' S SALT
4k7s CRYSTAL STRUCTURE OF ZN2-HUB (HUMAN UBIQUITIN) ADDUCT FROM A SOLUTION 35 MM ZINC ACETATE/1.3 MM HUB
4k7w CRYSTAL STRUCTURE OF ZN3-HUB(HUMAN UBIQUITIN) ADDUCT FROM A SOLUTION 100 MM ZINC ACETATE/1.3 MM HUB