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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SENP1 WITH THE BOUND COBALT
 
Authors :  V. Rimsa, T. Eadsforth, R. T. Hay, W. N. Hunter
Date :  26 Aug 10  (Deposition) - 08 Sep 10  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Cysteine Protease, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Rimsa, T. Eadsforth, R. T. Hay, W. N. Hunter
The Role Of Co2+ In The Crystallization Of Human Senp1 And Comments On The Limitations Of Automated Refinement Protocols
Acta Crystallogr. , Sect. F V. 67 442 2011
PubMed-ID: 21505236  |  Reference-DOI: 10.1107/S1744309111005835

(-) Compounds

Molecule 1 - SENTRIN-SPECIFIC PROTEASE 1
    ChainsA, B
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHISTEV30A
    Expression System StrainBL21(DE3) GOLD
    Expression System Taxid469008
    FragmentCATALYTIC FRAGMENT, RESIDUES 415-644
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCOBALT(II) ION, GLYCEROL
    SynonymSENTRIN/SUMO-SPECIFIC PROTEASE SENP1

 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  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2GOL6Ligand/IonGLYCEROL
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2GOL5Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:555 , TRP B:465BINDING SITE FOR RESIDUE GOL A1645
2AC2SOFTWARELYS A:543 , GLN B:569BINDING SITE FOR RESIDUE GOL A1646
3AC3SOFTWARELYS A:632BINDING SITE FOR RESIDUE GOL A1647
4AC4SOFTWAREGLN A:440 , TRP A:584 , LEU A:586 , HOH A:2003BINDING SITE FOR RESIDUE GOL A1648
5AC5SOFTWAREPRO A:421 , LYS A:616 , ASN A:621 , PHE A:630 , ARG A:633 , HOH A:2041BINDING SITE FOR RESIDUE GOL A1649
6AC6SOFTWARELYS B:429 , GLN B:458 , ASN B:461 , ASN B:464BINDING SITE FOR RESIDUE GOL B1645
7AC7SOFTWAREGLU A:430 , HIS A:640 , GLU B:430 , HIS B:640BINDING SITE FOR RESIDUE CO B1646

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XPH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XPH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XPH)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ULP_PROTEASEPS50600 Ubiquitin-like protease family profile.SENP1_HUMAN450-614
 
  2A:450-614
B:450-614
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ULP_PROTEASEPS50600 Ubiquitin-like protease family profile.SENP1_HUMAN450-614
 
  1A:450-614
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ULP_PROTEASEPS50600 Ubiquitin-like protease family profile.SENP1_HUMAN450-614
 
  1-
B:450-614

(-) Exons   (0, 0)

(no "Exon" information available for 2XPH)

(-) 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:227
 aligned with SENP1_HUMAN | Q9P0U3 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:227
                                   427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       
          SENP1_HUMAN   418 DEFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL 644
               SCOP domains d2xpha_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.........eee..eeehhhhhhh.......hhhhhhhhhhhhhhhh.......eee.....hhhhhh.hhhhhh......hhhhh.eeeeeeee..eeeeeeee....eeeee......hhhhhhhhhhhhhhhhhhhhh........eeee.............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------ULP_PROTEASE  PDB: A:450-614 UniProt: 450-614                                                                                                                        ------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xph A 418 DEFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL 644
                                   427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with SENP1_HUMAN | Q9P0U3 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:226
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638      
          SENP1_HUMAN   419 EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL 644
               SCOP domains d2xphb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------Peptidase_C48-2xphB01 B:464-642                                                                                                                                                    -- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------Peptidase_C48-2xphB02 B:464-642                                                                                                                                                    -- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhh.......eeeee..eeeehhhhhhhh.....hhhhhhhhhhhhhhhh.......eee...hhhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeee....eeeee......hhhhhhhhhhhhhhhhhhhhh........eeee..........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------ULP_PROTEASE  PDB: B:450-614 UniProt: 450-614                                                                                                                        ------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xph B 419 EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL 644
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638      

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XPH)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SENP1_HUMAN | Q9P0U3)
molecular function
    GO:0070139    SUMO-specific endopeptidase activity    Catalysis of the hydrolysis of peptide bonds between an alpha-carboxyl group and an alpha-amino group within the small conjugating protein SUMO.
    GO:0016929    SUMO-specific protease activity    Catalysis of the hydrolysis of SUMO, a small ubiquitin-related modifier, from previously sumoylated substrates.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    GO:0032435    negative regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0016926    protein desumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is cleaved from its target protein.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0010724    regulation of definitive erythrocyte differentiation    Any process that modulates the rate, frequency, or extent of definitive erythrocyte differentiation. Definitive erythrocyte differentiation occurs as part of the process of definitive hemopoiesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SENP1_HUMAN | Q9P0U32ckg 2ckh 2g4d 2iy0 2iy1 2iyc 2iyd 2xre

(-) Related Entries Specified in the PDB File

2ckg THE STRUCTURE OF SENP1 SUMO-2 CO-COMPLEX SUGGESTS A STRUCTURAL BASIS FOR DISCRIMINATION BETWEEN SUMO PARALOGUES DURING PROCESSING
2ckh SENP1-SUMO2 COMPLEX
2g4d CRYSTAL STRUCTURE OF HUMAN SENP1 MUTANT (C603S) IN COMPLEXWITH SUMO-1
2iy0 SENP1 (MUTANT) SUMO1 RANGAP
2iy1 SENP1 (MUTANT) FULL LENGTH SUMO1
2iyc SENP1 NATIVE STRUCTURE
2iyd SENP1 COVALENT COMPLEX WITH SUMO-2
2xre DETECTION OF COBALT IN PREVIOUSLY UNASSIGNED HUMAN SENP1 STRUCTURE