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

(-) Description

Title :  CRYSTAL STRUCTURE OF LSD2-NPAC WITH H3 IN SPACE GROUP P3221
 
Authors :  F. Chen, Z. Dong, J. Fang, Y. Yang, Z. Li, Y. Xu, H. Yang, P. Wang, R. Fang, Y
Date :  29 Aug 12  (Deposition) - 16 Jan 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A,B,C
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
 
Molecule 3 - HISTONE H3.3
    Chains: C
    Engineered: YES
    Fragment: UNP RESIDUES 2-22
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: H3K4 IS MUTATED TO MET
    Synonym: H3
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL2Ligand/IonGLYCEROL
3IOD6Ligand/IonIODIDE ION
4ZN3Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
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:419 , ARG A:420 , GLY A:435 , ALA A:436 , GLN A:437 , ILE A:438 , VAL A:598 , VAL A:627 , PRO A:628 , ILE A:659 , TRP A:757 , TRP A:762 , ALA A:766 , GLY A:794 , GLU A:795 , GLN A:803 , THR A:804 , VAL A:805 , ALA A:808 , HOH A:1102 , HOH A:1119 , HOH A:1126 , HOH A:1160 , HOH A:1253 , HOH A:1342BINDING SITE FOR RESIDUE FAD A 901
2AC2SOFTWARELYS A:128BINDING SITE FOR RESIDUE IOD A 904
3AC3SOFTWARELYS A:128BINDING SITE FOR RESIDUE IOD A 906
4AC4SOFTWARETRP A:422 , ARG A:434 , THR A:755 , ARG A:756 , TRP A:757 , ASP A:760 , HOH A:1186BINDING SITE FOR RESIDUE GOL A 908
5AC5SOFTWARELEU A:730 , GLN A:731 , MET A:734 , ARG A:738 , ASP A:748 , PRO A:749BINDING SITE FOR RESIDUE GOL A 909
6AC6SOFTWARECYS A:53 , CYS A:58 , HIS A:84 , HIS A:90BINDING SITE FOR RESIDUE ZN A 910
7AC7SOFTWARECYS A:65 , CYS A:73 , CYS A:92 , CYS A:95BINDING SITE FOR RESIDUE ZN A 911
8AC8SOFTWARECYS A:142 , CYS A:147 , CYS A:169 , CYS A:185BINDING SITE FOR RESIDUE ZN A 912

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:369 -Gly A:370
2Gly A:370 -Ala A:371
3Glu A:470 -Gly A:471
4Asn A:640 -Pro A:641

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GUS)

(-) 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:746
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................eeeee..eeeehhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhh...eee........eee.......hhhhhhhh...............hhhhh...hhhhhh.hhhhhhh...........hhhhhh..hhhhhh................................hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.................hhhhh..eeeee..hhhhhhhhhhhhhhh.eeeee...........ee.......ee....eee....hhhhhhhhhhh...ee......ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhh......eee....hhhhhhhhhh..eee....eeeee.....eeeee....eeee.eeee..hhhhhhhh..eee...hhhhhhhhhheeee..eeeeee.....hhhhhh...eeee...hhhhh.eeeeeee........eeeeee.hhhhhh....hhhhhhhhhhhhhhhhh.........eeee.hhhhh......eeee.....hhhhhhhhh.....eee.hhhhh.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gus A  49 GSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF 822
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      |266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816      
                                                                                                                                                                                                                    235|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                     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
                 4gus B 214 DPHFHHFLLSQT 225
                                   223  


Chain C from PDB  Type:PROTEIN  Length:20
                                                    
               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
                 4gus C   1 ARTMQTARKSTGGKAPRKQL  20
                                    10        20
   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 4GUS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 58)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:640 - Pro A:641   [ RasMol ]  
    Glu A:470 - Gly A:471   [ RasMol ]  
    Gly A:370 - Ala A:371   [ RasMol ]  
    Val A:369 - Gly A:370   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4gus
    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
  GLYR1_HUMAN | Q49A26
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  H33_HUMAN | P84243
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  KDM1B_HUMAN | Q8NB78
    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)
  1.-.-.-
    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
  GLYR1_HUMAN | Q49A26
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  H33_HUMAN | P84243
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  KDM1B_HUMAN | Q8NB78
    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
        GLYR1_HUMAN | Q49A26: 2uyy 4gur 4gut 4guu 4hsu
        H33_HUMAN | P84243: 1pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gnf 4gng 4gu0 4gur 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4tmp 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5ja4 5jjy 5jlb 5kdm 5x7x
        KDM1B_HUMAN | Q8NB78: 4fwe 4fwf 4fwj 4gu0 4gu1 4gur 4gut 4guu 4hsu

(-) Related Entries Specified in the PDB File

4gu1 4gur 4gut