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(-) Description

Title :  THE STRUCTURE OF THE C-TERMINAL HEME NITROBINDIN DOMAIN OF THAP DOMAIN-CONTAINING PROTEIN 4 FROM HOMO SAPIENS
 
Authors :  C. M. Bianchetti, C. A. Bingman, G. N. Phillips Jr. , Center For Eukar Structural Genomics (Cesg)
Date :  13 Jul 09  (Deposition) - 28 Jul 09  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Beta Barrel, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Heme, Thap Domain, Thap4, Dna-Binding, Metal-Binding, Phosphoprotein, Zinc-Finger, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Bianchetti, C. A. Bingman, G. N. Phillips
Structure Of The C-Terminal Heme-Binding Domain Of Thap Domain Containing Protein 4 From Homo Sapiens.
Proteins V. 79 1337 2011
PubMed-ID: 21387410  |  Reference-DOI: 10.1002/PROT.22944

(-) Compounds

Molecule 1 - THAP DOMAIN-CONTAINING PROTEIN 4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP68K
    Expression System Strain: B834 P(RARE2)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 415-577
    Gene: THAP4, CGI-36, PP238
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 14)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:32 , LEU A:33 , PHE A:36 , TYR A:38 , SER A:58 , MSE A:67 , HIS A:68 , PRO A:122 , ILE A:127 , ARG A:129 , MSE A:145 , HIS A:155 , LEU A:156 , HOH A:199 , HOH A:222 , HOH A:261 , HOH A:315BINDING SITE FOR RESIDUE HEM A 1
2AC2SOFTWARETHR B:32 , PHE B:36 , TYR B:38 , SER B:58 , MSE B:67 , HIS B:68 , GLN B:89 , PRO B:122 , ARG B:129 , MSE B:145 , HIS B:155 , LEU B:156 , HOH B:226 , HOH B:266 , HOH B:289 , HOH B:309 , HOH B:323BINDING SITE FOR RESIDUE HEM B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IA8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:23 -Pro A:24
2Glu A:121 -Pro A:122
3Asp B:23 -Pro B:24
4Glu B:121 -Pro B:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IA8)

(-) Exons   (0, 0)

(no "Exon" information available for 3IA8)

(-) 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:162
 aligned with THAP4_HUMAN | Q8WY91 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:162
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574  
          THAP4_HUMAN   415 PPKMNPVVEPLSWMLGTWLSDPPGAGTYPTLQPFQYLEEVHISHVGQPMLNFSFNSFHPDTRKPMHRECGFIRLKPDTNKVAFVSAQNTGVVEVEEGEVNGQELCIASHSIARISFAKEPHVEQITRKFRLNSEGKLEQTVSMATTTQPMTQHLHVTYKKVT 576
               SCOP domains d3ia8a_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhheeeee...eeeee..eeeeeeeeeeeee.....eeeeeeeee......eeeeeeeeeee.....eeeeeeee...eeeeeeeeee..eeeeeeeeeee........eeeeeeeeee.....eeeeeeeee..eeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ia8 A   3 PPKmNPVVEPLSWmLGTWLSDPPGAGTYPTLQPFQYLEEVHISHVGQPmLNFSFNSFHPDTRKPmHRECGFIRLKPDTNKVAFVSAQNTGVVEVEEGEVNGQELCIASHSIARISFAKEPHVEQITRKFRLNSEGKLEQTVSmATTTQPmTQHLHVTYKKVT 164
                               |    12   |    22        32        42        52        62    |   72        82        92       102       112       122       132       142  |    152       162  
                               |        16-MSE                             51-MSE          67-MSE                                                                       145-MSE  |            
                               6-MSE                                                                                                                                           152-MSE        


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with THAP4_HUMAN | Q8WY91 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:162
                                   424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574  
          THAP4_HUMAN   415 PPKMNPVVEPLSWMLGTWLSDPPGAGTYPTLQPFQYLEEVHISHVGQPMLNFSFNSFHPDTRKPMHRECGFIRLKPDTNKVAFVSAQNTGVVEVEEGEVNGQELCIASHSIARISFAKEPHVEQITRKFRLNSEGKLEQTVSMATTTQPMTQHLHVTYKKVT 576
               SCOP domains d3ia8b_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhheeeee...eeeee..eeeeeeeeeeeee.....eeeeeeeee......eeeeeeeeeee.....eeeeeeee...eeeeeeeeee..eeeeeeeeeee........eeeeeeeeee.....eeeeeeeee.....eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ia8 B   3 PPKmNPVVEPLSWmLGTWLSDPPGAGTYPTLQPFQYLEEVHISHVGQPmLNFSFNSFHPDTRKPmHRECGFIRLKPDTNKVAFVSAQNTGVVEVEEGEVNGQELCIASHSIARISFAKEPHVEQITRKFRLNSEGKLEQTVSmATTTQPmTQHLHVTYKKVT 164
                               |    12   |    22        32        42        52        62    |   72        82        92       102       112       122       132       142  |    152       162  
                               6-MSE    16-MSE                             51-MSE          67-MSE                                                                       145-MSE  |            
                                                                                                                                                                               152-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IA8)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (THAP4_HUMAN | Q8WY91)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.

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