Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SP100 AFTER INITIAL REFINEMENT WITH NO LIGAND MODELLED (STRUCTURE 74)
 
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 :  08 Feb 17  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
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, Transcription (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 - NUCLEAR AUTOANTIGEN SP-100
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SP100
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR DOT-ASSOCIATED SP100 PROTEIN,SPECKLED 100 KDA

 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  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3ZN5Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:705 , CYS A:708 , HIS A:725 , CYS A:728binding site for residue ZN A 901
2AC2SOFTWARECYS A:717 , CYS A:720 , CYS A:742 , CYS A:745binding site for residue ZN A 902
3AC3SOFTWARECYS A:754 , GLU A:756binding site for residue ZN A 903
4AC4SOFTWAREASN A:802 , ARG A:803 , TYR A:848 , HOH A:1028 , HOH A:1055 , HOH A:1100 , HOH A:1135 , HOH A:1138 , HOH A:1242 , ARG B:753 , PRO B:773 , GLU B:774 , EDO B:903 , HOH B:1235binding site for residue MES A 904
5AC5SOFTWAREGLU A:763 , ARG A:838 , HOH A:1048 , HOH A:1105 , HOH A:1122 , HOH A:1246binding site for residue EDO A 905
6AC6SOFTWARECYS B:705 , CYS B:708 , HIS B:725 , CYS B:728binding site for residue ZN B 901
7AC7SOFTWARECYS B:717 , CYS B:720 , CYS B:742 , CYS B:745binding site for residue ZN B 902
8AC8SOFTWAREMES A:904 , ARG B:746 , PRO B:773 , HOH B:1001 , HOH B:1026 , HOH B:1056 , HOH B:1126binding site for residue EDO B 903

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ile A:730 -Pro A:731
2Asn A:738 -Pro A:739
3Ile B:730 -Pro B:731
4Asn B:738 -Pro B:739
5Arg B:803 -Glu B:804

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5PYE)

(-) 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:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee......ee.................hhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pye A 701 NSNICEVCNKWGRLFCCDTCPRSFHEHCHIPSVEANKNPWSCIFCRIKTIQERCPESQSGHQESEVLMRQMLPEEQLKCEFLLLKVYCDSKSCFFASEPYYNREGSQGPQKPMWLNKVKTSLNEQMYTRVEGFVQDMRLIFHNHKEFYREDKFTRLGIQVQDIFEKNFRNIFAIQETS 878
                                   710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870        


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee......ee.................hhhhhhhhhhh.........hhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhh................hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pye B 700 ENSNICEVCNKWGRLFCCDTCPRSFHEHCHIPSVEANKNPWSCIFCRIKTIQERCPESQSGHQESEVLMRQMLPEEQLKCEFLLLKVYCDSKSCFFASEPYYNREGSQGPQKPMWLNKVKTSLNEQMYTRVEGFVQDMRLIFHNHKEFYREDKFTRLGIQVQDIFEKNFRNIFAIQE 876
                                   709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869
   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 5PYE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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 ]
    MES  [ 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
    Arg B:803 - Glu B:804   [ RasMol ]  
    Asn A:738 - Pro A:739   [ RasMol ]  
    Asn B:738 - Pro B:739   [ RasMol ]  
    Ile A:730 - Pro A:731   [ RasMol ]  
    Ile B:730 - Pro B:731   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5pye
    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
  SP100_HUMAN | P23497
    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)
  (no 'Enzyme Classificator' available)
    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
  SP100_HUMAN | P23497
    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
        SP100_HUMAN | P23497: 1h5p 4ptb 5fb0 5fb1 5pwc 5pwd 5pwe 5pwf 5pwg 5pwh 5pwi 5pwj 5pwk 5pwl 5pwm 5pwn 5pwo 5pwp 5pwq 5pwr 5pws 5pwt 5pwu 5pwv 5pww 5pwx 5pwy 5pwz 5px0 5px1 5px2 5px3 5px4 5px5 5px6 5px7 5px8 5px9 5pxa 5pxb 5pxc 5pxd 5pxe 5pxf 5pxg 5pxh 5pxi 5pxj 5pxk 5pxl 5pxm 5pxn 5pxo 5pxp 5pxq 5pxr 5pxs 5pxt 5pxu 5pxv 5pxw 5pxx 5pxy 5pxz 5py0 5py1 5py2 5py3 5py4 5py5 5py6 5py7 5py8 5py9 5pya 5pyb 5pyc 5pyd 5pyf 5pyg 5pyh 5pyi 5pyj 5pyk 5pyl 5pym 5pyn 5pyo 5pyp 5pyq 5pyr 5pys 5pyt 5pyu 5pyv 5pyw 5pyx 5pyy 5pyz 5pz0 5pz1 5pz2 5pz3 5pz4 5pz5 5pz6 5pz7 5pz8 5pz9 5pza 5pzb 5pzc 5pzd 5pze 5pzf 5pzg 5pzh 5pzi 5pzj

(-) Related Entries Specified in the PDB File

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