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 :  PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF JMJD2D AFTER INITIAL REFINEMENT WITH NO LIGAND MODELLED (STRUCTURE 122)
 
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 M. Vollmar, J. Ng, A. Szykowska, N. Burgess-Brown, P. E. Brennan, O. Co U. Oppermann, C. Bountra, C. H. Arrowsmith, A. Edwards, F. Von Delft
Date :  07 Feb 17  (Deposition) - 15 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Pandda, Sgc - Diamond I04-1 Fragment Screening, Jmj Domain, Epigenetics, Oxidoreductase (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
Pandda Analysis Group Deposition
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4D
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneKDM4D, JHDM3D, JMJD2D
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JUMONJI DOMAIN-CONTAINING PROTEIN 2D

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 15)

Asymmetric/Biological Unit (6, 15)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3NI1Ligand/IonNICKEL (II) ION
4OGA1Ligand/IonN-OXALYLGLYCINE
5SO43Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:238 , HIS A:244 , CYS A:310 , CYS A:312binding site for residue ZN A 401
02AC2SOFTWAREHIS A:192 , GLU A:194 , HIS A:280 , OGA A:404 , HOH A:672binding site for residue NI A 402
03AC3SOFTWAREASN A:65 , ILE A:66 , SER A:67 , GLU A:68 , ILE A:69 , VAL A:171binding site for residue MG A 403
04AC4SOFTWARETYR A:136 , TYR A:181 , HIS A:192 , GLU A:194 , SER A:200 , ASN A:202 , LYS A:210 , HIS A:280 , NI A:402 , EDO A:412 , HOH A:672 , HOH A:735binding site for residue OGA A 404
05AC5SOFTWARELYS A:150 , GLN A:151 , TRP A:152 , ASN A:153 , HIS A:156 , HOH A:613 , HOH A:720binding site for residue EDO A 405
06AC6SOFTWARETHR A:252 , ARG A:263 , HOH A:566binding site for residue EDO A 406
07AC7SOFTWAREGLU A:224 , ALA A:240 , PHE A:241 , LEU A:242 , TYR A:279 , SER A:308 , HOH A:509 , HOH A:539binding site for residue EDO A 407
08AC8SOFTWAREASP A:64 , ASN A:65 , ILE A:66 , SER A:67 , GLU A:68 , ARG A:82 , HOH A:562binding site for residue EDO A 408
09AC9SOFTWAREPHE A:118 , ILE A:264 , THR A:265 , HOH A:601binding site for residue EDO A 409
10AD1SOFTWARETRP A:57 , LYS A:58 , ALA A:59 , ARG A:60 , TYR A:63 , TYR A:203 , HOH A:505 , HOH A:567 , HOH A:611 , HOH A:650binding site for residue EDO A 410
11AD2SOFTWARESER A:80 , THR A:87 , CYS A:168 , LYS A:305 , HOH A:517 , HOH A:551binding site for residue EDO A 411
12AD3SOFTWARETYR A:179 , TYR A:181 , GLU A:194 , SER A:200 , ALA A:292 , ASN A:294 , OGA A:404 , HOH A:672binding site for residue EDO A 412
13AD4SOFTWAREARG A:102 , HIS A:103 , ASN A:106 , HOH A:506 , HOH A:527 , HOH A:632binding site for residue SO4 A 413
14AD5SOFTWAREARG A:60 , GLU A:61 , THR A:62 , ASN A:65 , HOH A:510 , HOH A:582 , HOH A:625 , HOH A:748binding site for residue SO4 A 414
15AD6SOFTWAREARG A:123 , LYS A:124 , LYS A:127 , ASN A:128binding site for residue SO4 A 415

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5PL1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5PL1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5PL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5PL1)

(-) Exons   (0, 0)

(no "Exon" information available for 5PL1)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee........hhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pl1 A  11 AQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQD 341
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 

   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 5PL1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5PL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5PL1)

(-) Gene Ontology  (18, 18)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OGA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5pl1)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5pl1
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KDM4D_HUMAN | Q6B0I6
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  KDM4D_HUMAN | Q6B0I6
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KDM4D_HUMAN | Q6B0I63dxt 3dxu 4d6q 4d6r 4d6s 4hon 4hoo 5f5a 5f5c 5fp4 5fp7 5fp8 5fp9 5fpa 5fpb 5ph0 5ph1 5ph2 5ph3 5ph4 5ph5 5ph6 5ph7 5ph8 5ph9 5pha 5phb 5phc 5phd 5phe 5phf 5phg 5phh 5phi 5phj 5phk 5phl 5phm 5phn 5pho 5php 5phq 5phr 5phs 5pht 5phu 5phv 5phw 5phx 5phy 5phz 5pi0 5pi1 5pi2 5pi3 5pi4 5pi5 5pi6 5pi7 5pi8 5pi9 5pia 5pib 5pic 5pid 5pie 5pif 5pig 5pih 5pii 5pij 5pik 5pil 5pim 5pin 5pio 5pip 5piq 5pir 5pis 5pit 5piu 5piv 5piw 5pix 5piy 5piz 5pj0 5pj1 5pj2 5pj3 5pj4 5pj5 5pj6 5pj7 5pj8 5pj9 5pja 5pjb 5pjc 5pjd 5pje 5pjf 5pjg 5pjh 5pji 5pjj 5pjk 5pjl 5pjm 5pjn 5pjo 5pjp 5pjq 5pjr 5pjs 5pjt 5pju 5pjv 5pjw 5pjx 5pjy 5pjz 5pk0 5pk1 5pk2 5pk3 5pk4 5pk5 5pk6 5pk7 5pk8 5pk9 5pka 5pkb 5pkc 5pkd 5pke 5pkf 5pkg 5pkh 5pki 5pkj 5pkk 5pkl 5pkm 5pkn 5pko 5pkp 5pkq 5pkr 5pks 5pkt 5pku 5pkv 5pkw 5pkx 5pky 5pkz 5pl0 5pl2 5pl3 5pl4 5pl5 5pl6 5pl7 5pl8 5pl9 5pla 5plb 5plc 5pld 5ple 5plf 5plg 5plh 5pli 5plj 5plk 5pll 5plm 5pln 5plo 5plp 5plq 5plr 5pls 5plt 5plu 5plv 5plw 5plx 5ply 5plz 5pm0 5pm1 5pm2 5pm3 5pm4 5pm5 5pm6 5pm7 5pm8 5pm9 5pma 5pmb 5pmc 5pmd 5pme 5pmf 5pmg 5pmh 5pmi 5pmj 5pmk 5pml 5pmm 5pmn 5pmo 5pmp 5pmq 5pmr 5pms 5pmt 5pmu 5pmv 5pmw 5pmx 5pmy 5pmz 5pn0 5pn1 5pn2 5pn3 5pn4 5pn5 5pn6 5pn7 5pn8 5pn9 5pna 5pnb 5pnc 5pnd 5pne 5pnf 5png 5pnh 5pni 5pnj 5pnk 5pnl 5pnm 5pnn 5pno 5pnp 5pnq 5pnr 5pns 5pnu 5pnv 5pnw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5PL1)