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(-) Description

Title :  HUMAN A20 OTU DOMAIN WITH I325N AND ALKYLATED C103 TO 2.5A RESOLUTION
 
Authors :  D. B. Langley, D. Christ, S. T. Grey
Date :  11 Sep 15  (Deposition) - 21 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Ubiquitin Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. B. Langley, D. Christ, D. T. Grey
Human A20 Otu Domain With I325N And Acetamidylated C103 At 2. 50 Angstroms Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3
    ChainsA, B, C, D, E, F
    EC Number3.4.19.12, 6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX P61
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTNFAIP3, OTUD7C
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHE ACTIVE SITE CYSTEINE, C103, HAS BEEN ACETAMIDYLATED WITH IODOACETAMIDE.
    SynonymTNF ALPHA-INDUCED PROTEIN 3,OTU DOMAIN-CONTAINING PROTEIN 7C,PUTATIVE DNA-BINDING PROTEIN A20,ZINC FINGER PROTEIN A20

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A  D  
Biological Unit 2 (1x) BC   
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1YCM6Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1YCM2Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1YCM2Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1YCM2Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 5DOD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:267 -Pro A:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DOD)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhh..........hhhhhhhhhhhhh..eeee....eee.....hhhhh....eeeeee..eeeeeee.........eee.ee...ee......hhhhhhhhhhhhhhhh.eee....eeee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dod A   5 VLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQNWNDEWDNLIKMASTDTLQYNSLEEIHIFVLCNILRRPIIVISKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPLNNAAKLDEANLPKEINLVDDYFELVQHEYKKWQ 357
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144     ||166       176  ||   192       202       228       238       248       258       268       278|      291       301       311 ||    331       341       351      
                                                                                                                            103-YCM                                        150|             179|                      211|                                               278|                            313|                                 
                                                                                                                                                                            163              186                       228                                                282                             324                                 

Chain B from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhh..eeee....eee.....hhhhh....eeeeee..eeeeeee.........eee...........hhhhhhhhhhhhhhhh.ee..eee......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dod B   5 VLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSNWNDEWDNLIKMASTDLQYNSLEEIHIFVLCNILRRPIIVISKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNEDLKVHFLTDPENEMKEKLLKEYLMVIENAAKLDEANLPKEINLVDDYFELVQHEYKKWQE 358
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144    || 167       177||     194       204      |230       240       250       260       270      |286       296       306    || 330       340       350        
                                                                                                                            103-YCM                                       149|            178|                      211|                                              277|                        311|                                
                                                                                                                                                                           163             186                       228                                               284                         326                                

Chain C from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhhhhhhh..eeee...eee.....hhhhh....eeeeee..eeeeeee......eee.ee..ee......hhhhhhhhhhhhhhhh.eee...eeee......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dod C   4 QVLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFNWNDEWDNLIKMASTDTLQYNSLEEIHIFVLCNILRRPIIVISVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDEIRAVPLVNRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPNNAAKLDEANLPKEINLVDDYFELVQHEYKKWQE 358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       163       173     ||189       199       209 ||    236       246       256       269       283       293       303       313|      334       344       354    
                                                                                                                             103-YCM                                          152|             179|                      211|                                 265|     277|                            313|                                 
                                                                                                                                                                               163              186                       229                                  269      282                             325                                 

Chain D from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh........hhhhhhhhhhhhh..eeeee......eee.....hhhhh....eeeeee..eeeeeee.......eee...........hhhhhhhhhhhhhhhh.eee...eeee......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dod D   5 VLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQDTRNWNDEWDNLIKMASTDTQYNSLEEIHIFVLCNILRRPIIVISDKLKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDPEIRAVPLVFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPNNAAKLDEANLPKEINLVDDYFELVQHEYKKWQE 358
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144     ||163       173     ||190       200       210  ||   233       243       253       263 ||    275||     291       301       311 ||    332       342       352      
                                                                                                                            103-YCM                                        150|                179|                       213|                                   265|     276|                           313|                                 
                                                                                                                                                                            160                 187                        227                                    268      283                            325                                 

Chain E from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhee...ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh............ee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhh..eeee....eee.....hhhhh....eeeeee..eeeeee....eee..........hhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dod E   6 LPQALYLSNMRKAVKIRERTPEDIFKPHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESNWNDEWDNLIKMASTDQYNSLEEIHIFVLCNILRRPIIVISKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTEIRAVPLVEDLKVHFLTDPENEMKEKLLKEYLMVINAAKLDEANLPKEINLVDDYFELVQHEYKKWQE 358
                                    15        25      ||40        50        60        70        80        90       100  |    110       120       130       140     ||166       176 ||    194       204      |230       240       250       260 ||    276|      293       303      |328       338       348       358
                                                     32|                                                              103-YCM                                    146|            178|                     211|                               262|    276|                       310|                                
                                                      38                                                                                                          163             187                      228                                269     284                        326                                

Chain F from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...ee........ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhh.............hhhhhhhhhhhhh..eeee..eee.....hhhhh....eeeeee..eeeeeee...ee........hhhhhhhhhhhhhhhh.ee..ee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dod F   6 LPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWGVQDTDLVLRKALFSTLNFKFRWIKMASTDLQYNSLEEIHIFVLCNILRRPIIVIVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKAVPLVLKVHFLTDPENEMKEKLLKEYLMVINNAAKLDEANLPKEINLVDDYFELVQHEYKK 355
                                    15        25        35        45        55        65        75        85        95       105       115       125    || 141||     187       197       207  ||   235       245       255       272   ||  291       301       325       335       345       355
                                                                                                                           103-YCM                    130|  142|   178|                     210|                                264| 276|                     310|                              
                                                                                                                                                       137   172    186                      229                                 272  286                      325                              

   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 5DOD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (76, 76)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNAP3_HUMAN | P215802eqe 2eqf 2eqg 2vfj 3dkb 3oj3 3oj4 3vuw 3vux 3vuy 3zjd 3zje 3zjf 3zjg 4zrh 4zs5 5lrx

(-) Related Entries Specified in the PDB File

4zrh 4ZRH CONTAINS THE SAME PROTEIN MODIFIED IN THE SAME WAY, AND CRYSTALLIZING IN THE SAME SPACE GROUP. THIS PARTICULAR DATASET IS SUPERIOR BOTH IN TERMS OF DATA METRICS, RESOLUTION, AND THE CLARITY OF MAPS FROM WHICH THE MODEL WAS REFINED