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(-) Description

Title :  CRYSTAL STRUCTURE OF ZN3-E16V HUMAN UBIQUITIN (HUB) MUTANT ADDUCT, FROM A SOLUTION 70 MM ZINC ACETATE/20% V/V TFE/1.3 MM E16V HUB
 
Authors :  F. Simona, F. Giuseppe
Date :  04 Apr 17  (Deposition) - 26 Apr 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  E16V Mutant, Ligase, Ubiquitination, Proteasome Degradation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Simona, M. Calvaresi, V. Mangini, G. Falini, A. Bottoni, G. Natile, F. Arnesano
Ubiquitin Conformer Selection And Aggregation Controlled By Single-Point Mutation, Metal Ion Concentration And Dielectric Constant.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYUBIQUITIN-B
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBB
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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  (5, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3ETF1Ligand/IonTRIFLUOROETHANOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN9Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3ETF-1Ligand/IonTRIFLUOROETHANOL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3ETF1Ligand/IonTRIFLUOROETHANOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3ETF-1Ligand/IonTRIFLUOROETHANOL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:6 , THR A:66 , HIS A:68 , ZN A:107 , LYS B:6 , HIS B:68binding site for residue ACT A 101
02AC2SOFTWAREVAL A:16 , GLU A:18 , ASP A:21 , LYS A:29 , ZN A:105 , GLU B:18binding site for residue ACT A 102
03AC3SOFTWAREASP A:39 , ZN A:106 , HOH A:245 , HIS C:68 , ACT C:101binding site for residue ACT A 103
04AC4SOFTWAREGLU A:18 , ACT A:108 , ZN B:105 , ASP C:21 , HOH C:222binding site for residue ZN A 104
05AC5SOFTWAREASP A:21 , ACT A:102 , HOH A:213 , GLU B:18 , PEG B:102 , ZN B:105binding site for residue ZN A 105
06AC6SOFTWAREASP A:39 , ACT A:103 , HIS C:68 , ACT C:101binding site for residue ZN A 106
07AC7SOFTWAREHIS A:68 , ACT A:101 , LYS B:6 , HIS B:68binding site for residue ZN A 107
08AC8SOFTWAREGLU A:18 , ZN A:104 , HOH A:205 , HOH A:224 , ZN B:105 , VAL C:16 , GLU C:18 , ASP C:21 , LYS C:29binding site for residue ACT A 108
09AC9SOFTWAREMET A:1 , GLU B:51 , ASP C:32binding site for residue ZN A 109
10AD1SOFTWAREHOH A:205 , VAL B:16 , GLU B:18 , ASP B:21 , LYS B:29 , ZN B:104 , HOH B:215 , HOH B:216 , GLU C:18binding site for residue ACT B 101
11AD2SOFTWARESER A:20 , ASP A:21 , ASN A:25 , ZN A:105 , HOH A:213 , SER B:20 , ASN B:25 , ZN B:105 , HOH B:202 , SER C:20 , ASP C:21 , ASN C:25 , HOH C:222binding site for residue PEG B 102
12AD3SOFTWAREMET B:1 , HOH B:228 , HOH B:278binding site for residue ZN B 103
13AD4SOFTWAREASP B:21 , ACT B:101 , ZN B:105 , HOH B:216 , GLU C:18binding site for residue ZN B 104
14AD5SOFTWAREGLU A:18 , ZN A:104 , ZN A:105 , ACT A:108 , HOH A:205 , HOH A:213 , GLU B:18 , PEG B:102 , ZN B:104 , HOH B:216 , GLU C:18 , HOH C:222binding site for residue ZN B 105
15AD6SOFTWARELYS B:11 , GLU B:34 , HOH B:258 , HOH B:269binding site for residue ZN B 106
16AD7SOFTWARELEU B:8 , ILE B:36 , GLN B:40 , HOH B:250 , HOH C:248binding site for residue ETF B 107
17AD8SOFTWAREASP A:39 , ACT A:103 , ZN A:106 , ALA C:46 , HIS C:68 , HOH C:230binding site for residue ACT C 101
18AD9SOFTWARESER B:20 , THR B:55 , HOH C:206 , HOH C:209binding site for residue EDO C 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NLJ)

(-) 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:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- 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
                  5nlj A  1 MQIFVKTLTGKTITLVVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
                                    10        20        30        40        50        60        70 


Chain B from PDB  Type:PROTEIN  Length:71
                                                                                                      
               SCOP domains ----------------------------------------------------------------------- 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
                  5nlj B  1 MQIFVKTLTGKTITLVVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
                                    10        20        30        40        50        60        70 


Chain C from PDB  Type:PROTEIN  Length:72
                                                                                                       
               SCOP domains ------------------------------------------------------------------------ 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
                  5nlj C  1 MQIFVKTLTGKTITLVVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
                                    10        20        30        40        50        60        70
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5NLJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (89, 89)

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 Related Entries

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

UniProtKB/Swiss-Prot
        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 5gob 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 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1y 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5

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