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(-) Description

Title :  CRYSTAL STRUCTURE OF LSD2-NPAC WITH TRANYLCYPROMINE
 
Authors :  F. Chen, Z. Dong, J. Fang, Y. Yang, Z. Li, Y. Xu, H. Yang, P. Wang, Y. Xu
Date :  29 Aug 12  (Deposition) - 16 Jan 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Histone Demethylase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Fang, F. Chen, Z. Dong, D. Hu, A. J. Barbera, E. A. Clark, J. Fang, Y. Yang, P. Mei, M. Rutenberg, Z. Li, Y. Zhang, Y. Xu, H. Yang, P. Wang, M. D. Simon, Q. Zhou, J. Li, M. P. Marynick, X. Li, H. Lu, U. B. Kaiser, R. E. Kingston, Y. Xu, Y. G. Shi
Lsd2/Kdm1B And Its Cofactor Npac/Glyr1 Endow A Structural And Molecular Model For Regulation Of H3K4 Demethylation
Mol. Cell V. 49 558 2013
PubMed-ID: 23260659  |  Reference-DOI: 10.1016/J.MOLCEL.2012.11.019

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC HISTONE DEMETHYLASE 1B
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 51-822
    Gene: LSD2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LSD2, FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 1, LYSINE-SPECIFIC HISTONE DEMETHYLASE 2
 
Molecule 2 - PUTATIVE OXIDOREDUCTASE GLYR1
    Chains: B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 152-268
    Gene: GLYR1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NPAC, 3-HYDROXYISOBUTYRATE DEHYDROGENASE-LIKE PROTEIN, CYTOKINE-LIKE NUCLEAR FACTOR N-PAC, GLYOXYLATE REDUCTASE 1 HOMOLOG, NUCLEAR PROTEIN NP60, NUCLEAR PROTEIN OF 60 KDA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FA91Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[(3R,3AS,7AR)-10,11-DIMETHYL-1,4,6-TRIOXO-3-PHENYL-2,3,5,6,7,7A-HEXAHYDRO-1H-BENZO[G]PYRROLO[2,1-E]PTERIDIN-8(4H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGENDIPHOSPHATE
2ZN3Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:388 , GLY A:389 , GLY A:391 , PRO A:392 , ALA A:393 , LEU A:411 , GLU A:412 , ALA A:413 , LYS A:414 , GLY A:418 , GLY A:419 , ARG A:420 , ALA A:436 , GLN A:437 , ILE A:438 , TYR A:545 , VAL A:598 , THR A:626 , VAL A:627 , PRO A:628 , TRP A:757 , TRP A:762 , ALA A:766 , TYR A:767 , GLY A:794 , GLU A:795 , GLN A:803 , THR A:804 , VAL A:805 , ALA A:808 , HOH A:1102 , HOH A:1121 , HOH A:1195 , HOH A:1246BINDING SITE FOR RESIDUE FA9 A 901
2AC2SOFTWARECYS A:53 , CYS A:58 , HIS A:84 , HIS A:90BINDING SITE FOR RESIDUE ZN A 902
3AC3SOFTWARECYS A:65 , CYS A:73 , CYS A:92 , CYS A:95BINDING SITE FOR RESIDUE ZN A 903
4AC4SOFTWARECYS A:142 , CYS A:147 , CYS A:169 , CYS A:185BINDING SITE FOR RESIDUE ZN A 904

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:470 -Gly A:471
2Asn A:640 -Pro A:641

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GUU)

(-) 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:740
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................eee.....eeehhhhhhhhh....hhhhhhhhhhhhhhh.....hhhhhhhhhh...eee........eee.......hhhhhhhh........hhhhh...hhhhhh...................hhhhhh..hhhhhh................................hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..........hhhhh..hhhhhh.eeeee..hhhhhhhhhhhhhhh.eeeee...........ee.......ee....eee....hhhhhhhhhhh...ee......ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...........hhhhhh......eee....hhhhhhhhhh...ee....eeeee.....eeeee....eeee.eeee..hhhhhhh...eee...hhhhhhhhhheeee..eeeeee.....hhhhhh...eeee...hhhhh.eeeeeee........eeeeee.hhhhhhhhh.hhhhhhhhhhhhhhhhh.........eeee.hhhhh......eeee.....hhhhhhhhh.....eee.hhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4guu A  47 PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAA 821
                                    56        66        76        86        96       106       116       126       136       146       156       166       183       193       203       213       223       233 ||    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
                                                                                                                                                         174|                                                  235|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                                          182                                                   264                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4guu B 214 DPHFHHFLLSQT 225
                                   223
   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 4GUU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:640 - Pro A:641   [ RasMol ]  
    Glu A:470 - Gly A:471   [ RasMol ]  
 

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  4guu
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  GLYR1_HUMAN | Q49A26
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  KDM1B_HUMAN | Q8NB78
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLYR1_HUMAN | Q49A26: 2uyy 4gur 4gus 4gut 4hsu
        KDM1B_HUMAN | Q8NB78: 4fwe 4fwf 4fwj 4gu0 4gu1 4gur 4gus 4gut 4hsu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4GUU)