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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PEPTIDE(PRO)9 BOUND COMPLEX OF N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-238) TYPE I FROM HUMAN
 
Authors :  J. Anantharajan, M. K. Koski, R. K. Wierenga
Date :  14 Jun 13  (Deposition) - 09 Oct 13  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Oxidoreductase, Tetratricopeptide Repeat Motif, Coiled-Coil, Proline Rich Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Anantharajan, M. K. Koski, P. Kursula, R. Hieta, U. Bergmann, J. Myllyharju, R. K. Wierenga
The Structural Motifs For Substrate Binding And Dimerizatio Of The Alpha Subunit Of Collagen Prolyl 4-Hydroxylase
Structure V. 21 2107 2013
PubMed-ID: 24207127  |  Reference-DOI: 10.1016/J.STR.2013.09.005

(-) Compounds

Molecule 1 - PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
    ChainsA
    EC Number1.14.11.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET22B
    Expression System Vector TypePLASMID
    FragmentCOLLAGEN BINDING DOMAIN, RESIDUES 18-255
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym4-PH ALPHA-1, PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4- DIOXYGENASE SUBUNIT ALPHA-1, PROLYL-4 HYDROXYLASE TYPE I
 
Molecule 2 - POLY PROLINE PEPTIDE
    ChainsC
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4BTB)

(-) Sites  (0, 0)

(no "Site" information available for 4BTB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 1)

Asymmetric/Biological Unit (2, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.P4HA1_HUMAN205-238  1A:188-221
2TPR_REGIONPS50293 TPR repeat region circular profile.P4HA1_HUMAN205-238  1A:188-221

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003948901aENSE00001372871chr10:74856732-74856524209P4HA1_HUMAN-00--
1.2bENST000003948902bENSE00001170044chr10:74834673-74834566108P4HA1_HUMAN1-26261A:2-98
1.3ENST000003948903ENSE00001102025chr10:74833585-7483348997P4HA1_HUMAN26-58331A:9-4133
1.4ENST000003948904ENSE00001102018chr10:74831938-74831787152P4HA1_HUMAN58-109521A:41-92 (gaps)52
1.5ENST000003948905ENSE00000987124chr10:74828741-74828604138P4HA1_HUMAN109-155471A:92-13847
1.6ENST000003948906ENSE00001169998chr10:74813348-74813109240P4HA1_HUMAN155-235811A:138-21881
1.7aENST000003948907aENSE00001169991chr10:74811007-74810811197P4HA1_HUMAN235-300661A:218-23619
1.8ENST000003948908ENSE00001169986chr10:74806859-74806683177P4HA1_HUMAN301-359590--
1.9ENST000003948909ENSE00001169981chr10:74804809-7480473971P4HA1_HUMAN360-383240--
1.11bENST0000039489011bENSE00001169972chr10:74790128-74790029100P4HA1_HUMAN383-416340--
1.12aENST0000039489012aENSE00001169965chr10:74776657-7477660454P4HA1_HUMAN417-434180--
1.13ENST0000039489013ENSE00001169956chr10:74774047-7477398266P4HA1_HUMAN435-456220--
1.14bENST0000039489014bENSE00001169951chr10:74770795-7477072769P4HA1_HUMAN457-479230--
1.15aENST0000039489015aENSE00001169944chr10:74769661-7476956597P4HA1_HUMAN480-512330--
1.16aENST0000039489016aENSE00001382372chr10:74768050-747669821069P4HA1_HUMAN512-534230--

(-) 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:231
 aligned with P4HA1_HUMAN | P13674 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:235
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     
          P4HA1_HUMAN    19 PGFFTSIGQMTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDPEGFVGHPVNAFKLMKRLNTEWSELENLVLKDMSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLPGVKHKSFLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYIMA 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhh............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPR_REGION  PDB: A:188-221        --------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPR  PDB: A:188-221               --------------- PROSITE (2)
           Transcript 1 (1) 1.2b    -------------------------------Exon 1.4  PDB: A:41-92 (gaps) UniProt: 58-109       ---------------------------------------------Exon 1.6  PDB: A:138-218 UniProt: 155-235                                        ------------------ Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.3  PDB: A:9-41            --------------------------------------------------Exon 1.5  PDB: A:92-138 UniProt: 109-155       -------------------------------------------------------------------------------Exon 1.7a           Transcript 1 (2)
                 4btb A   2 PGFFTSIGQMTDLIHTEKDLVTSLKDYIKAEEDKLEQIKKWAEKLDRLTSTATKDP----GHPVNAFKLMKRLNTEWSELENLVLKDMSDGFISNLTIQRQYFPNDEDQVGAAKALLRLQDTYNLDTDTISKGNLPGVKHKSFLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNLKYFEYIMA 236
                                    11        21        31        41        51     |   -|       71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     
                                                                                  57   62                                                                                                                                                                              

Chain C from PDB  Type:PROTEIN  Length:9
                                         
               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
                 4btb C   0 PPPPPPPPP   8

   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 4BTB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P4HA1_HUMAN | P13674)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
    GO:0004656    procollagen-proline 4-dioxygenase activity    Catalysis of the reaction: procollagen L-proline + 2-oxoglutarate + O2 = procollagen trans-4-hydroxy-L-proline + succinate + CO2.
    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:0030199    collagen fibril organization    Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0018401    peptidyl-proline hydroxylation to 4-hydroxy-L-proline    The modification of peptidyl-proline to form 4-hydroxy-L-proline; catalyzed by procollagen-proline,2-oxoglutarate-4-dioxygenase.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0016222    procollagen-proline 4-dioxygenase complex    A protein complex that catalyzes the formation of procollagen trans-4-hydroxy-L-proline and succinate from procollagen L-proline and 2-oxoglutarate, requiring Fe2+ and ascorbate. Contains two alpha subunits that contribute to most parts of the catalytic sites, and two beta subunits that are identical to protein-disulfide isomerase.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P4HA1_HUMAN | P136741tjc 2v5f 2yq8 4bt8 4bt9 4bta

(-) Related Entries Specified in the PDB File

4bt8 CRYSTAL STRUCTURE OF THE APO FORM OF N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL- 4 HYDROXYLASE TYPE I FROM HUMAN
4bt9 CRYSTAL STRUCTURE OF THE PEPTIDE(PRO-PRO-GLY)3 BOUND COMPLEX OF N- TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-238 ) TYPE I FROM HUMAN
4bta CRYSTAL STRUCTURE OF THE PEPTIDE(PRO-PRO-GLY)3 BOUND COMPLEX OF N- TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE (RESIDUES 1-244 ) TYPE I FROM HUMAN