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(-) Description

Title :  STRUCTURE OF THE BROMODOMAIN OF HUMAN ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2 (ATAD2) IN COMPLEX WITH THYMINE
 
Authors :  A. Chaikuad, I. Felletar, F. Von Delft, C. H. Arrowsmith, A. M. Edwards C. Bountra, S. Knapp, Structural Genomics Consortium (Sgc)
Date :  06 Jul 14  (Deposition) - 23 Jul 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics Consortium (Sgc), Signaling Protein, Bromodomain, Actyl-Lysine Binding, Atpase Family Aaa Domain-Containing Protein 2, Epigenetics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, A. M. Petros, O. Fedorov, J. Xu, S. Knapp
Structure-Based Approaches Towards Identification Of Fragments For The Low-Druggability Atad2 Bromodomain
Medchemcomm V. 5 1843 2014
PubMed: search  |  Reference-DOI: 10.1039/C4MD00237G

(-) Compounds

Molecule 1 - ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
    Chains: A
    EC Number: 3.6.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21-R3-PRARE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BROMODOMAIN (RESIDUES 981-1108)
    Gene: ATAD2, L16, PRO2000
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AAA NUCLEAR COREGULATOR CANCER-ASSOCIATED PROTEIN, ANCCA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2SO42Ligand/IonSULFATE ION
3TDR1Ligand/IonTHYMINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2SO42Ligand/IonSULFATE ION
3TDR1Ligand/IonTHYMINE
Biological Unit 2 (3, 20)
No.NameCountTypeFull Name
1EDO14Ligand/Ion1,2-ETHANEDIOL
2SO44Ligand/IonSULFATE ION
3TDR2Ligand/IonTHYMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:987 , ARG A:990 , ARG A:994 , ARG A:1067 , ARG A:1072 , HOH A:1455BINDING SITE FOR RESIDUE SO4 A 1201
02AC2SOFTWARELYS A:1037 , LYS A:1042 , HOH A:1462 , HOH A:1463BINDING SITE FOR RESIDUE SO4 A 1202
03AC3SOFTWAREGLU A:988 , LEU A:1093 , ASP A:1094 , PHE A:1097 , HOH A:1415 , HOH A:1417BINDING SITE FOR RESIDUE EDO A 1203
04AC4SOFTWAREHIS A:998 , GLU A:1092 , ASP A:1094 , HOH A:1416 , HOH A:1501BINDING SITE FOR RESIDUE EDO A 1204
05AC5SOFTWARECYS A:1057 , CYS A:1079 , ARG A:1082 , ASP A:1083 , HOH A:1367BINDING SITE FOR RESIDUE EDO A 1205
06AC6SOFTWAREARG A:1082 , ASP A:1083 , TYR A:1086BINDING SITE FOR RESIDUE EDO A 1206
07AC7SOFTWAREASP A:1039 , LEU A:1040 , HIS A:1041 , HOH A:1468BINDING SITE FOR RESIDUE EDO A 1207
08AC8SOFTWAREGLY A:1070 , ASP A:1071 , HOH A:1346 , HOH A:1477BINDING SITE FOR RESIDUE EDO A 1208
09AC9SOFTWAREASP A:1083 , ALA A:1087 , HOH A:1311 , HOH A:1482BINDING SITE FOR RESIDUE EDO A 1209
10BC1SOFTWAREVAL A:1013 , ASN A:1064 , ILE A:1074 , HOH A:1347BINDING SITE FOR RESIDUE TDR A 1210

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4QSU)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qsu A  979 SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR 1108
                                   988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108
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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  (0, 0)

(no "SCOP Domain" information available for 4QSU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (14, 14)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ATAD2_HUMAN | Q6PL18: 3dai 4qsp 4qsq 4qsr 4qss 4qst 4qsv 4qsw 4qsx 4qut 4quu 4tt2 4tt4 4tt6 4tte 4tu4 4tu6 4tyl 4tz2 4tz8 5a5n 5a5o 5a5p 5a5q 5a5r 5a81 5a82 5a83 5epb 5f36 5f3a 5lj0

(-) Related Entries Specified in the PDB File

4qsp 4qsq 4qsr 4qss 4qst 4qsv 4qsw 4qsx