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(-) Description

Title :  PHYSIOLOGICAL DIMER HPP PRECURSOR
 
Authors :  G. Rudenko, E. Bonten, A. D'Azzo, W. G. J. Hol
Date :  12 Jun 96  (Deposition) - 21 Apr 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Carboxypeptidase, Serine Carboxypeptidase, Protective Protein, Glycoprotein, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Rudenko, E. Bonten, A. D'Azzo, W. G. Hol
Three-Dimensional Structure Of The Human 'Protective Protein': Structure Of The Precursor Form Suggests A Comple Activation Mechanism.
Structure V. 3 1249 1995
PubMed-ID: 8591035  |  Reference-DOI: 10.1016/S0969-2126(01)00260-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUMAN PROTECTIVE PROTEIN
    Cell LineSF21
    ChainsA, B
    EC Number3.4.16.5
    EngineeredYES
    Expression SystemSF21 INSECT CELLS
    Expression System GeneHUPP54
    GeneHUPP54
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsBACULOVIRUS MEDIATED OVER-EXPRESSION. SEE BONTEN ET AL. 1995, J.B.C. 270, P. 26441-26445
    SynonymPROTECTIVE PROTEIN/CATHEPSIN A, CARBOXYPEPTIDASE L

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:117 , GLU A:120 , ARG A:343 , LEU A:345 , NDG A:3011 , GLN B:4BINDING SITE FOR RESIDUE NAG A 3010
2AC2SOFTWARENAG A:3010BINDING SITE FOR RESIDUE NDG A 3011
3AC3SOFTWAREPRO A:77 , ASN A:305 , THR A:307 , HOH A:3028BINDING SITE FOR RESIDUE NAG A 3020
4AC4SOFTWAREASN B:117 , LEU B:345 , NAG B:3031BINDING SITE FOR RESIDUE NAG B 3030
5AC5SOFTWARENAG B:3030BINDING SITE FOR RESIDUE NAG B 3031
6AC6SOFTWAREPRO B:77 , ASN B:305BINDING SITE FOR RESIDUE NAG B 3040
7CATUNKNOWNSER A:150 , ASP A:372 , HIS A:429 , SER B:150 , ASP B:372 , HIS B:429CATALYTIC TRIAD SERINE CARBOXYPEPTIDASE.

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:60 -A:334
2A:212 -A:228
3A:213 -A:218
4A:253 -A:303
5B:60 -B:334
6B:212 -B:228
7B:213 -B:218
8B:253 -B:303

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:57 -Pro A:58
2Ser A:100 -Pro A:101
3Gly B:57 -Pro B:58
4Ser B:100 -Pro B:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (12, 24)

Asymmetric/Biological Unit (12, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_001385Q49RPPGB_HUMANDisease (GSL)137854541A/BQ21R
02UniProtVAR_063018S51YPPGB_HUMANDisease (GSL)  ---A/BS23Y
03UniProtVAR_001386W65RPPGB_HUMANDisease (GSL)28934603A/BW37R
04UniProtVAR_001387S90LPPGB_HUMANDisease (GSL)137854542A/BS62L
05UniProtVAR_063019V132MPPGB_HUMANDisease (GSL)137854545A/BV104M
06UniProtVAR_063020L236PPPGB_HUMANDisease (GSL)137854546A/BL208P
07UniProtVAR_001388Y249NPPGB_HUMANDisease (GSL)137854544A/BY221N
08UniProtVAR_001389Y395CPPGB_HUMANDisease (GSL)137854543A/BY367C
09UniProtVAR_063021M406TPPGB_HUMANDisease (GSL)137854548A/BM378T
10UniProtVAR_063022G439SPPGB_HUMANDisease (GSL)137854547A/BG411S
11UniProtVAR_001390F440VPPGB_HUMANDisease (GSL)137854540A/BF412V
12UniProtVAR_063023K453EPPGB_HUMANDisease (GSL)137854549A/BK425E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_SER_SERPS00131 Serine carboxypeptidases, serine active site.PPGB_HUMAN174-181
 
  2A:146-153
B:146-153
2CARBOXYPEPT_SER_HISPS00560 Serine carboxypeptidases, histidine active site.PPGB_HUMAN447-464
 
  2A:419-436
B:419-436

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2eENST000003724592eENSE00001457871chr20:44520053-44520401349PPGB_HUMAN1-65652A:1-37
B:1-37
37
37
1.3ENST000003724593ENSE00000662429chr20:44520555-44520666112PPGB_HUMAN65-102382A:37-74
B:37-74
38
38
1.4aENST000003724594aENSE00000845061chr20:44520912-4452096251PPGB_HUMAN103-119172A:75-91
B:75-91
17
17
1.5ENST000003724595ENSE00000845062chr20:44521037-4452112387PPGB_HUMAN120-148292A:92-120
B:92-120
29
29
1.6ENST000003724596ENSE00000845063chr20:44521364-44521519156PPGB_HUMAN149-200522A:121-172
B:121-172
52
52
1.7bENST000003724597bENSE00000662432chr20:44521859-4452195092PPGB_HUMAN201-231312A:173-203
B:173-203
31
31
1.8aENST000003724598aENSE00000662433chr20:44522627-4452271185PPGB_HUMAN231-259292A:203-231
B:203-231
29
29
1.9bENST000003724599bENSE00002189764chr20:44523289-4452338092PPGB_HUMAN260-289302A:232-261
B:232-261 (gaps)
30
30

(-) 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:452
 aligned with PPGB_HUMAN | P10619 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:452
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478  
           PPGB_HUMAN    29 APDQDEIQRLPGLAKQPSFRQYSGYLKGSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVPSHFRYEKDTVVVQDLGNIFTRLPLKRMWHQALLRSGDKVRMDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPY 480
               SCOP domains d1ivya_ A: Human 'protective protein', HPP                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ivyA00 A:1-452  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeeee....eeeeeeee..........eeeee........hhhhh.....eee......eee.........eeeee...................hhhhhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhhhhh.....hhhhhhhhhhh.............hhhhhhhhhhhhhhh....................eeee..eeee...................hhhh..eeee.......hhhhhhh..hhhhhh..............hhhhhh........hhhhhhhhhh...eeeeeee.......hhhhhhhhhh....eeeeeeeeeee.....eeeeeeeeee..eeeeee......hhhh.hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------R-Y-------------R------------------------L-----------------------------------------M-------------------------------------------------------------------------------------------------------P------------N-------------------------------------------------------------------------------------------------------------------------------------------------C----------T--------------------------------SV------------E--------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYP-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_SER_HI---------------- PROSITE
           Transcript 1 (1) Exon 1.2e  PDB: A:1-37 UniProt: 1-65 -------------------------------------Exon 1.4a        Exon 1.5  PDB: A:92-120      Exon 1.6  PDB: A:121-172 UniProt: 149-200           Exon 1.7b  PDB: A:173-203      ----------------------------Exon 1.9b  PDB: A:232-261     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: A:37-74 UniProt: 65-102--------------------------------------------------------------------------------------------------------------------------------Exon 1.8a  PDB: A:203-231    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1ivy A   1 APDQDEIQRLPGLAKQPSFRQYSGYLKSSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVPSHFRYEKDTVVVQDLGNIFTRLPLKRMWHQALLRSGDKVRMDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPY 452
                                    10        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       350       360       370       380       390       400       410       420       430       440       450  

Chain B from PDB  Type:PROTEIN  Length:450
 aligned with PPGB_HUMAN | P10619 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:452
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478  
           PPGB_HUMAN    29 APDQDEIQRLPGLAKQPSFRQYSGYLKGSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVPSHFRYEKDTVVVQDLGNIFTRLPLKRMWHQALLRSGDKVRMDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPY 480
               SCOP domains d1ivyb_ B: Human 'protective protein', HPP                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1ivyB00 B:1-452  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeeee....eeeeeeee..........eeeee........hhhhh.....eee......eee.........eeeee...................hhhhhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhhhhh.....hhhhhhhhhhh.............hhhhhhhhhhhhhhh..................--......eeee.........................eeee.......hhhhhhh..hhhhhh..............hhhhhh........hhhhhhhhhh...eeeeeee.......hhhhhhhhhh....eeeeeeeeeee.....eeeeeeeeee..eeeeee......hhhh.hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------R-Y-------------R------------------------L-----------------------------------------M-------------------------------------------------------------------------------------------------------P------------N-------------------------------------------------------------------------------------------------------------------------------------------------C----------T--------------------------------SV------------E--------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYP-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_SER_HI---------------- PROSITE
           Transcript 1 (1) Exon 1.2e  PDB: B:1-37 UniProt: 1-65 -------------------------------------Exon 1.4a        Exon 1.5  PDB: B:92-120      Exon 1.6  PDB: B:121-172 UniProt: 149-200           Exon 1.7b  PDB: B:173-203      ----------------------------Exon 1.9b UniProt: 260-289    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.3  PDB: B:37-74 UniProt: 65-102--------------------------------------------------------------------------------------------------------------------------------Exon 1.8a  PDB: B:203-231    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1ivy B   1 APDQDEIQRLPGLAKQPSFRQYSGYLKSSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVP--FRYEKDTVVVQDLGNIFTRLPLKRMWHQALLRSGDKVRMDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPY 452
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       | -|      270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450  
                                                                                                                                                                                                                                                                                           258  |                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                              261                                                                                                                                                                                               

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  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/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IVY)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPGB_HUMAN | P10619)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0004308    exo-alpha-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
    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:0004185    serine-type carboxypeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0061684    chaperone-mediated autophagy    The autophagy process which begins when chaperones and co-chaperones recognize a KFERQ-related motif and unfold the substrate protein. The proteins are then transported to the lysosome where they are degraded.
    GO:0006687    glycosphingolipid metabolic process    The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:1904714    regulation of chaperone-mediated autophagy    Any process that modulates the frequency, rate or extent of chaperone-mediated autophagy.
    GO:0031647    regulation of protein stability    Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0098575    lumenal side of lysosomal membrane    The side (leaflet) of the lysosomal membrane that faces the lumen.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPGB_HUMAN | P106193bp4 3bp7 3bxn 4az0 4az3 4ci9 4cia 4cib 4mws 4mwt

(-) Related Entries Specified in the PDB File

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