Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF BRD1 IN COMPLEX WITH N11063A
 
Authors :  N. M. Pearce, T. Krojer, R. Talon, A. R. Bradley, M. Fairhead, R. Sethi, N E. Maclean, P. Collins, J. Brandao-Neto, A. Douangamath, Z. Renjie, A J. Ng, P. E. Brennan, O. Cox, C. Bountra, C. H. Arrowsmith, A. Edwards, F Delft
Date :  07 Feb 17  (Deposition) - 15 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pandda, Sgc - Diamond I04-1 Fragment Screening, Bromodomain, Epigenetics, Xchemexplorer, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. M. Pearce, T. Krojer, A. R. Bradley, P. Collins, R. Nowak, R. Talon, B. Marsden, S. Kelm, J. Shi, D. Deane, F. Von Delft
A Multi-Crystal Method For Extracting Obscured Crystallographic States From Conventionally Uninterpretable Electron Density
Nat Commun 2017
PubMed: search

(-) Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BRD1, BRL, BRPF2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BR140-LIKE PROTEIN,BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
18TJ2Ligand/IonN-METHYLTHIENO[2,3-B]PYRIDINE-2-CARBOXAMIDE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
18TJ1Ligand/IonN-METHYLTHIENO[2,3-B]PYRIDINE-2-CARBOXAMIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
18TJ1Ligand/IonN-METHYLTHIENO[2,3-B]PYRIDINE-2-CARBOXAMIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:109 , ASN A:110 , EDO A:202 , 8TJ A:203binding site for residue EDO A 201
2AC2SOFTWAREILE A:54 , PHE A:55 , VAL A:59 , PHE A:116 , EDO A:201 , 8TJ A:203 , HOH A:301 , HOH A:321binding site for residue EDO A 202
3AC3SOFTWAREILE A:54 , PHE A:55 , VAL A:59 , VAL A:64 , ASN A:110 , PHE A:116 , EDO A:201 , EDO A:202 , HOH A:301 , MET B:23binding site for residue 8TJ A 203
4AC4SOFTWARELYS A:108 , HOH A:309 , HOH A:325 , MET B:107 , ASN B:110 , TYR B:117binding site for residue NA B 201
5AC5SOFTWAREILE B:54 , PHE B:55 , CYS B:106 , ASN B:110 , PHE B:116 , 8TJ B:204 , HOH B:304binding site for residue EDO B 202
6AC6SOFTWARELEU B:92 , GLU B:96 , LEU B:131 , ARG B:135 , HOH B:305binding site for residue EDO B 203
7AC7SOFTWAREGLU A:63 , ILE B:54 , VAL B:59 , VAL B:64 , CYS B:106 , ASN B:110 , PHE B:116 , EDO B:202 , HOH B:304 , HOH B:313 , HOH B:355 , HOH B:390binding site for residue 8TJ B 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5POG)

(-) 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:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5pog A  22 SMEQVAMELRLTELTRLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVD 139
                                    31        41        51        61        71        81        91       101       111       121       131        


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pog B  22 SMEQVAMELRLTELTRLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVDSIGLE 144
                                    31        41        51        61        71        81        91       101       111       121       131       141
   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 5POG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    8TJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5pog)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5pog
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  BRD1_HUMAN | O95696
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  BRD1_HUMAN | O95696
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BRD1_HUMAN | O95696: 2ku3 2l43 2lq6 3lyi 3rcw 4z02 5ame 5amf 5fg6 5gk9 5n49 5pnx 5pny 5pnz 5po0 5po1 5po2 5po3 5po4 5po5 5po6 5po7 5po8 5po9 5poa 5pob 5poc 5pod 5poe 5pof 5poh 5poi 5poj 5pok 5pol 5pom 5pon 5poo 5pop 5poq 5por 5pos 5pot 5pou 5pov 5pow 5pox 5poy 5poz 5pp0 5pp1 5pp2 5pp3 5pp4 5pp5 5pp6 5pp7 5pp8 5pp9 5ppa 5ppb 5ppc 5ppd 5ppe 5ppf 5ppg 5pph 5ppi 5ppj 5ppk 5ppl 5ppm 5ppn 5ppo 5ppp 5ppq 5ppr 5pps 5ppt 5ppu 5ppv 5ppw 5ppx 5ppy 5ppz 5pq0 5pq1 5pq2 5pq3 5pq4 5pq5 5pq6 5pq7 5pq8 5pq9 5pqa 5pqb 5pqc 5pqd 5pqe 5pqf 5pqg 5pqh 5pqi 5pqj 5pqk 5pql 5pqm 5pqn 5pqo 5pqp 5pqq 5pqr 5pqs 5pqt 5pqu 5pqv 5pqw 5pqx 5pqy 5pqz 5pr0 5pr1 5pr2 5pr4 5pr5 5pr6 5pr7 5pr8 5pr9 5pra 5prb 5prd 5pre 5prf 5prg 5prh 5pri 5prj 5prk 5prl 5prm 5pro 5prp 5prq 5prr 5prs 5prt 5pru 5prv 5prw 5prx 5pry 5prz 5ps0 5ps1 5ps2 5ps3 5ps4 5ps5 5ps6 5ps7 5ps8 5ps9 5psa 5psb 5psc 5psd 5pse 5psf 5psg 5psh 5psi 5psj 5psk 5psl 5psm 5psn 5pso 5psp 5psq 5psr 5pss 5pst 5psu 5psv 5psw 5psx 5psy 5psz 5pt0 5pt1 5pt2 5pt3 5pt4 5pt5 5pt6 5pt7 5pt8 5pt9 5pta 5ptb 5ptc 5pte 5ptf 5ptg 5pth 5ptj 5ptk 5ptl 5ptm 5ptn 5pto 5ptq 5ptr 5pts 5ptt 5ptu 5ptv 5ptw 5ptx 5pty 5ptz 5pu0 5pu1 5pu2 5pu3 5pu4 5pu5 5pu6 5pu7 5pu8 5pu9 5pua 5pub 5puc 5pud 5pue 5puf 5pug 5puh 5pui 5puj 5puk 5pul 5pum 5pun 5puo 5pup 5puq 5pur 5pus 5put 5puu 5puv 5puw 5pux 5puy 5puz 5pv0 5pv1 5pv2 5pv3 5pv4 5pv5 5pv6 5pv7 5pv8 5pv9 5pva 5pvb 5pvc 5pvd 5pve 5pvf 5pvg 5pvh 5pvi 5pvj 5pvk 5pvl 5pvm 5pvn 5pvo 5pvp 5pvq 5pvr 5pvs 5pvt 5pvu 5pvv 5pvw 5pvx 5pvy 5pvz 5pw0 5pw1 5pw2 5pw3 5pw4 5pw5 5pw6 5pw7 5pw8 5pw9 5pwa 5pwb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5POG)