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
(-)Biological Unit 3
(-)Biological Unit 4
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SCP1 BOUND TO TRANS-PROLINE PEPTIDOMIMETIC CTD PHOSPHO-SER5 PEPTIDE
 
Authors :  J. E. Mayfield, Y. Zhang
Date :  26 Feb 15  (Deposition) - 16 Sep 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,C  (1x)
Biol. Unit 4:  B,D  (1x)
Keywords :  Phosphatase, Peptidomimetic, Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Mayfield, S. Fan, S. Wei, M. Zhang, B. Li, A. D. Ellington, F. A. Etzkorn, Y. J. Zhang
Chemical Tools To Decipher Regulation Of Phosphatases By Proline Isomerization On Eukaryotic Rna Polymerase Ii.
Acs Chem. Biol. V. 10 2405 2015
PubMed-ID: 26332362  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B00296

(-) Compounds

Molecule 1 - CARBOXY-TERMINAL DOMAIN RNA POLYMERASE II POLYPEPTIDE A SMALL PHOSPHATASE 1
    Chains: A, B
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 76-254
    Gene: CTDSP1, NIF3, NLIIF, SCP1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR LIM INTERACTOR-INTERACTING FACTOR 3,NLI-INTERACTING FACTOR 3,SMALL C-TERMINAL DOMAIN PHOSPHATASE 1,SMALL CTD PHOSPHATASE 1
 
Molecule 2 - PEPTIDOMIMETIC CTD PHOSPHO-SER5 PEPTIDE
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (1x): A C 
Biological Unit 4 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
14CG2Mod. Amino Acid(1R,2Z)-2-[(2R)-2-AMINO-3-(PHOSPHONOOXY)PROPYLIDENE]CYCLOPENTANECARBOXYLIC ACID
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14CG1Mod. Amino Acid(1R,2Z)-2-[(2R)-2-AMINO-3-(PHOSPHONOOXY)PROPYLIDENE]CYCLOPENTANECARBOXYLIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14CG1Mod. Amino Acid(1R,2Z)-2-[(2R)-2-AMINO-3-(PHOSPHONOOXY)PROPYLIDENE]CYCLOPENTANECARBOXYLIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
14CG1Mod. Amino Acid(1R,2Z)-2-[(2R)-2-AMINO-3-(PHOSPHONOOXY)PROPYLIDENE]CYCLOPENTANECARBOXYLIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
14CG1Mod. Amino Acid(1R,2Z)-2-[(2R)-2-AMINO-3-(PHOSPHONOOXY)PROPYLIDENE]CYCLOPENTANECARBOXYLIC ACID
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:96 , ASP A:98 , ASN A:207 , HOH A:411 , HOH A:412 , 4CG C:5binding site for residue MG A 301
2AC2SOFTWAREASN B:96 , ASP B:98 , ASN B:207 , HOH B:408 , HOH B:411 , 4CG D:5 , HOH D:101binding site for residue MG B 301
3AC3SOFTWAREASN A:96 , LEU A:97 , ASP A:98 , THR A:152 , ALA A:153 , SER A:154 , LYS A:190 , MG A:301 , HOH A:411 , HOH A:412 , THR C:4binding site for Ligand 4CG C 5 bound to THR C 4
4AC4SOFTWAREASN B:96 , LEU B:97 , ASP B:98 , THR B:152 , ALA B:153 , ARG B:178 , LYS B:190 , MG B:301 , HOH B:411 , THR D:4 , HOH D:101binding site for Ligand 4CG D 5 bound to THR D 4

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YGY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YGY)

(-) 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:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...eeee......eeee........eeeeeee..eeeeeeeee..hhhhhhhhhhhhheeeee...hhhhhhhhhhhhh....eeeeehhhhheee..eee.hhhhh..hhh.eeeee.hhhhhh.hhh.eee..........hhhhhhhhhhhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ygy A  77 QYLLPEAKAQDSDKICVVINLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLR 255
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         


Chain B from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee......eeee........eeeeeee..eeeeeeeee..hhhhhhhhhhhhheeeee...hhhhhhhhhhhhh....eeeeehhhhheee..eee.hhhhh..hhh.eeeee.hhhhhh.hhh.eee..........hhhhhhhhhhhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ygy B  77 QYLLPEAKAQDSDKICVVINLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLR 255
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               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
                 4ygy C   2 SPTx   5
                               |
                               5-4CG


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               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
                 4ygy D   2 SPTx   5
                               |
                               |
                               5-4CG
   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 4YGY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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
    4CG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ygy)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4ygy
    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
  CTDS1_HUMAN | Q9GZU7
    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)
  3.1.3.16
    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
  CTDS1_HUMAN | Q9GZU7
    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
        CTDS1_HUMAN | Q9GZU7: 1t9z 1ta0 2ghq 2ght 3l0b 3l0c 3l0y 3pgl 4yh1

(-) Related Entries Specified in the PDB File

4ygx 4yh1