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(-) Description

Title :  CRYSTAL STRUCTURE OF SMARCA4 BROMODOMAIN IN COMPLEX WITH MPD
 
Authors :  G. Lolli, A. Caflisch
Date :  15 Oct 15  (Deposition) - 16 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Four Helical Bundle, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Lolli, A. Caflisch
High-Throughput Fragment Docking Into The Baz2B Bromodomain Efficient In Silico Screening For X-Ray Crystallography.
Acs Chem. Biol. V. 11 800 2016
PubMed-ID: 26942307  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B00914

(-) Compounds

Molecule 1 - TRANSCRIPTION ACTIVATOR BRG1
    Chains: A, B, C
    EC Number: 3.6.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: BROMODOMAIN, UNP RESIDUES 1451-1580
    Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FIRST TWO RESIDUES SM DERIVE FROM THE EXPRESSION TAG
    Synonym: ATP-DEPENDENT HELICASE SMARCA4,BRG1-ASSOCIATED FACTOR 190A, BAF190A,MITOTIC GROWTH AND TRANSCRIPTION ACTIVATOR,PROTEIN BRG-1, PROTEIN BRAHMA HOMOLOG 1,SNF2-BETA,SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A MEMBER 4

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:1485 , PRO A:1489 , TYR A:1497 , PHE A:1539 , ASN A:1540 , MPD A:1602 , HOH A:1701binding site for residue MRD A 1601
2AC2SOFTWAREPHE A:1485 , PRO A:1489 , PHE A:1539 , ASN A:1540 , MRD A:1601 , HOH A:1701binding site for residue MPD A 1602
3AC3SOFTWAREVAL B:1484 , PHE B:1485 , TYR B:1497 , ALA B:1536 , ASN B:1540 , MPD B:1602binding site for residue MRD B 1601
4AC4SOFTWAREVAL B:1484 , PHE B:1485 , TYR B:1497 , ALA B:1536 , ASN B:1540 , MRD B:1601binding site for residue MPD B 1602
5AC5SOFTWAREGLU B:1548 , PRO C:1489 , PHE C:1539 , ASN C:1540 , MPD C:1602 , HOH C:1704 , HOH C:1716binding site for residue MRD C 1601
6AC6SOFTWAREGLU B:1548 , PRO C:1489 , PHE C:1539 , ASN C:1540 , MRD C:1601 , HOH C:1704 , HOH C:1716binding site for residue MPD C 1602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EA1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EA1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EA1)

(-) Exons   (0, 0)

(no "Exon" information available for 5EA1)

(-) 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:114
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                5ea1 A 1452 SPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIE 1565
                                  1461      1471      1481      1491      1501      1511      1521      1531      1541      1551      1561    


Chain B from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ea1 B 1451 LSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSEGEESEEE 1578
                                  1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570        


Chain C from PDB  Type:PROTEIN  Length:119
                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                5ea1 C 1451 LSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDD 1569
                                  1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560
   Legend:   → Mismatch (orange background)
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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 5EA1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EA1)

(-) Gene Ontology  (59, 59)

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  5ea1
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 Related Entries

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        SMCA4_HUMAN | P51532: 2grc 2h60 3uvd 5dkd

(-) Related Entries Specified in the PDB File

5e9y MPD BOUND TO A DIFFERENT BROMODOMAIN