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(-) Description

Title :  PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF BRD1 AFTER INITIAL REFINEMENT WITH NO LIGAND MODELLED (STRUCTURE 111)
 
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) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneBRD1, BRL, BRPF2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBR140-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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:109 , ASN A:110 , EDO A:202binding site for residue EDO A 201
2AC2SOFTWAREILE A:54 , PHE A:55 , VAL A:59 , CYS A:106 , PHE A:116 , EDO A:201 , HOH A:302 , HOH A:303 , HOH A:313binding site for residue EDO A 202
3AC3SOFTWARELYS A:108 , HOH A:328 , HOH A:365 , MET B:107 , ASN B:110 , TYR B:117binding site for residue NA B 201
4AC4SOFTWAREILE B:54 , TYR B:109 , ASN B:110 , HOH B:301 , HOH B:306binding site for residue EDO B 202
5AC5SOFTWARELEU B:92 , GLU B:96 , LEU B:131 , ARG B:135 , HOH B:302binding site for residue EDO B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5PS4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5PS4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5PS4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5PS4)

(-) Exons   (0, 0)

(no "Exon" information available for 5PS4)

(-) 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:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ps4 A  22 SMEQVAMELRLTELTRLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVDSIG 142
                                    31        41        51        61        71        81        91       101       111       121       131       141 

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
                 5ps4 B  22 SMEQVAMELRLTELTRLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVDSIGLE 144
                                    31        41        51        61        71        81        91       101       111       121       131       141   

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  - → 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 5PS4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5PS4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5PS4)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRD1_HUMAN | O956962ku3 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 5pog 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 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 5PS4)