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(-) Description

Title :  CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PEPTIDE 13
 
Authors :  M. Kkuchi, Y. Amano, S. Sato, S. Yokoyama, N. Umezawa, T. Higuchi, T. Ume
Date :  14 Nov 16  (Deposition) - 12 Apr 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Demethylase, Amine Oxidase, Chromatin, Histone, Fad, Corepressor, Oxidoreductase-Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Amano, M. Kikuchi, S. Sato, S. Yokoyama, T. Umehara, N. Umezawa, T. Higuchi
Development And Crystallographic Evaluation Of Histone H3 Peptide With N-Terminal Serine Substitution As A Potent Inhibitor Of Lysine-Specific Demethylase 1.
Bioorg. Med. Chem. 2017
PubMed-ID: 28336409  |  Reference-DOI: 10.1016/J.BMC.2017.03.016

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 172-833
    Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2
 
Molecule 2 - REST COREPRESSOR 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: KRX
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 308-440
    Gene: RCOR1, KIAA0071, RCOR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN COREST
 
Molecule 3 - PEPTIDE (HSE)RTMQTARKSTGGKAPRKQLK
    Chains: C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL2Ligand/IonGLYCEROL
3HSE1Mod. Amino AcidL-HOMOSERINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:285 , GLY A:287 , VAL A:288 , SER A:289 , LEU A:307 , GLU A:308 , ALA A:309 , ARG A:310 , GLY A:314 , GLY A:315 , ARG A:316 , LEU A:329 , GLY A:330 , ALA A:331 , MET A:332 , VAL A:333 , THR A:588 , VAL A:590 , THR A:624 , LEU A:625 , PRO A:626 , VAL A:637 , TRP A:751 , TRP A:756 , SER A:760 , TYR A:761 , GLY A:800 , GLU A:801 , ALA A:809 , THR A:810 , VAL A:811 , ALA A:814 , HOH A:1002 , HOH A:1003 , HOH A:1005 , HOH A:1016 , HOH A:1022 , HOH A:1026 , HOH A:1038binding site for residue FAD A 901
2AC2SOFTWAREGLY A:409 , GLU A:413 , ARG A:526 , LEU A:544 , ARG A:688binding site for residue GOL A 902
3AC3SOFTWAREARG A:312 , SER A:749 , ARG A:750 , ASP A:754binding site for residue GOL A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H6R)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:240 -Pro A:241
2Pro A:470 -Pro A:471
3Gln A:633 -Pro A:634
4Val A:640 -Pro A:641

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H6R)

(-) Exons   (0, 0)

(no "Exon" information available for 5H6R)

(-) Sequences/Alignments

Asymmetric/Biological 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:662
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.......hhhhhhhhhhhhhhh....................eeeee..hhhhhhhhhhhhhh..eeeee...........eeee..eeee....ee......hhhhhhhhh...eee......ee.......hhhhhhhhhhhhhhhhhhhhhhhhh....ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..............hhhhh.....eee....hhhhhhhhh..eee..eeeeeeee....eeeeeee......eeeeee.eeee..hhhhhhh.....eee...hhhhhhhhhhhee...eeeeee...........eeee.........eeeeee......eeeeee.hhhhhhhh..hhhhhhhhhhhhhhhhhh........eeee.............ee......hhhhhhhhh.................eee.hhhhh.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h6r A 172 SGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM 833
                                   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831  


Chain B from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5h6r B 309 KPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE 440
                                   318       328       338       348       358       368       378       388       398       408       418       428       438  


Chain C from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 5h6r C   1 xRTMQTARKSTGGK  14
                            |       10    
                            1-HSE
   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 5H6R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H6R)

(-) Gene Ontology  (71, 85)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ala A:240 - Pro A:241   [ RasMol ]  
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    Val A:640 - Pro A:641   [ RasMol ]  
 

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  5h6r
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM1A_HUMAN | O60341: 2com 2dw4 2ejr 2h94 2hko 2iw5 2l3d 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaj 2xaq 2xas 2y48 2z3y 2z5u 3abt 3abu 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4czz 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 4xbf 5afw 5h6q 5it3 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lgu 5lhg 5lhh 5lhi 5x60
        RCOR1_HUMAN | Q9UKL0: 2iw5 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaj 2xaq 2xas 2y48 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 4xbf 5h6q 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lgu 5lhg 5lhh 5lhi 5x60

(-) Related Entries Specified in the PDB File

5h6q