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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIGH AFFINITY HETERODIMER OF HIF2 ALPHA AND ARNT C-TERMINAL PAS DOMAINS IN COMPLEX WITH AN INACTIVE BENZOXADIAZOLE ANTAGONIST
 
Authors :  T. H. Scheuermann, K. H. Gardner
Date :  27 Aug 12  (Deposition) - 03 Apr 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Keywords :  Pas Fold, Transcription, Protein-Protein Interactions, Nucleus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Rogers, L. Bayeh, T. H. Scheuermann, J. Longgood, J. Key, J. Naidoo, L. Melito, C. Shokri, D. E. Frantz, R. K. Bruick, K. H. Gardner, J. B. Macmillan, U. K. Tambar
Development Of Inhibitors Of The Pas-B Domain Of The Hif-2 Alpha Transcription Factor
J. Med. Chem. V. 56 1739 2013
PubMed-ID: 23363003  |  Reference-DOI: 10.1021/JM301847Z

(-) Compounds

Molecule 1 - ENDOTHELIAL PAS DOMAIN-CONTAINING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-GB1
    Expression System Strain: BL21(DE3) CONDONPLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HIF2 PAS-B DOMAIN, UNP RESIDUES 239-350
    Gene: BHLHE73, EPAS1, HIF2, HIF2A, MOP2, PASD2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPAS-1, BASIC-HELIX-LOOP-HELIX-PAS PROTEIN MOP2, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 73, BHLHE73, HIF-1-ALPHA-LIKE FACTOR, HLF, HYPOXIA-INDUCIBLE FACTOR 2-ALPHA, HIF-2-ALPHA, HIF2-ALPHA, MEMBER OF PAS PROTEIN 2, PAS DOMAIN-CONTAINING PROTEIN 2
 
Molecule 2 - ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-GB1
    Expression System Strain: BL21(DE3) CONDONPLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ARNT PAS-B DOMAIN, UNP RESIDUES 356-470
    Gene: ARNT, BHLHE2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARNT PROTEIN, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 2, BHLHE2, DIOXIN RECEPTOR, NUCLEAR TRANSLOCATOR, HYPOXIA-INDUCIBLE FACTOR 1-BETA, HIF-1-BETA, HIF1-BETA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
10XB1Ligand/IonN-(3-FLUOROPHENYL)-4-NITRO-2,1,3-BENZOXADIAZOL-5-AMINE
2PE81Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
10XB1Ligand/IonN-(3-FLUOROPHENYL)-4-NITRO-2,1,3-BENZOXADIAZOL-5-AMINE
2PE81Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:246 , HIS A:248 , MET A:252 , ALA A:277 , TYR A:281 , MET A:289 , SER A:292 , HIS A:293 , TYR A:307 , MET A:309 , THR A:321 , ASN A:341BINDING SITE FOR RESIDUE 0XB A 401
2AC2SOFTWARETYR A:278 , THR A:290 , HIS A:293 , GLN A:294 , THR A:298 , TYR B:386 , GLU B:390 , LYS B:394 , GLU B:398BINDING SITE FOR RESIDUE PE8 A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GS9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GS9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GS9)

(-) Exons   (0, 0)

(no "Exon" information available for 4GS9)

(-) 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:107
                                                                                                                                           
               SCOP domains d4gs9a_ A: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeee.....eeee.hhhhhhhh.hhhhhh..hhhhhh...hhhhhhhhhhhhhhhheee...eeee.....eeeeeeeeeee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4gs9 A   0 FKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYPQCIMCVNYVLSEIE 348
                              ||   245       255       265       275       285       295       305       315       325 ||    341       
                              2|                                                                                     327|              
                             239                                                                                      334              


Chain B from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains d4gs9b_ B: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeee..hhhhhhh.hhhhh...hhhhhh...hhhhhhhhhhhhh......eeeeeeee.....eeeeeeeeeee.........eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 4gs9 B 360 PTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSS 468
                                   369       379       389       399       409       419       429       439       449       459
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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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GS9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GS9)

(-) Gene Ontology  (60, 79)

Asymmetric Unit(hide GO term definitions)

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  ARNT_HUMAN | P27540
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  EPAS1_HUMAN | Q99814
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARNT_HUMAN | P27540: 1d7g 1x0o 2a24 2arn 2b02 2hv1 2k7s 3f1n 3f1o 3f1p 3h7w 3h82 4eq1 4ghi 4h6j 4lpz 4pky 4xt2 5nj8 5tbm 5ufp 5v0l
        EPAS1_HUMAN | Q99814: 1p97 2a24 3f1n 3f1o 3f1p 3h7w 3h82 4ghi 4pky 4xt2 5kiz 5tbm 5ufp

(-) Related Entries Specified in the PDB File

1p97 NMR STRUCTURE OF THE HIF2ALPHA PAS-B DOMAIN.
1x0o NMR STRUCTURE OF THE ARNT PAS-B DOMAIN.
2a24 NMR-GUIDED MODEL OF THE WT HIF2 PAS-B HETERODIMER
2b02 CRYSTAL STRUCTURE OF THE ARNT PAS-B DOMAIN
3f1n TERNARY COMPLEX OF CRYOSOLVENT WITH AN ENHANCED AFFINITY HIF2 PAS-B HETERODIMER
3f1o TERNARY COMPLEX OF LIGAND THS-044 WITH AN ENHANCED AFFINITY HIF2 PAS-B HETERODIMER
3f1p CRYSTAL STRUCTURE OF AN ENHANCED AFFINITY HIF2 PAS-B HETERODIMER, UNLIGANDED.
3h7w TERNARY COMPLEX OF LIGAND THS-017 WITH AN ENHANCED AFFINITY HIF2 PAS-B HETERODIMER
3h82 TERNARY COMPLEX OF LIGAND THS-020 WITH AN ENHANCED AFFINITY HIF2 PAS-B HETERODIMER
4ghi TERNARY COMPLEX OF LIGAND JN-128-022 WITH AN ENHANCED AFFINITY HIF2 PAS-B HETERODIMER