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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CATHEPSIN X
 
Authors :  G. Guncar, I. Klemencic, B. Turk, V. Turk, A. Karaoglanovic-Carmona, L D. Turk
Date :  07 Feb 00  (Deposition) - 15 Mar 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Papain-Like, Cysteine Protease, Carboxypeptidase, Cathepsin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Guncar, I. Klemencic, B. Turk, V. Turk, A. Karaoglanovic-Carmona, L. Juliano, D. Turk
Crystal Structure Of Cathepsin X: A Flip-Flop Of The Ring O His23 Allows Carboxy-Monopeptidase And Carboxy-Dipeptidase Activity Of The Protease.
Structure Fold. Des. V. 8 305 2000
PubMed-ID: 10745011  |  Reference-DOI: 10.1016/S0969-2126(00)00108-8

(-) Compounds

Molecule 1 - CATHEPSIN X
    ChainsA, B
    EC Number3.4.18.1
    OrganLIVER
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1EF7)

(-) Sites  (0, 0)

(no "Site" information available for 1EF7)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:28 -A:71
2A:65 -A:103
3A:93 -A:109
4A:112 -A:118
5A:153 -A:235
6B:28 -B:71
7B:65 -B:103
8B:93 -B:109
9B:112 -B:118
10B:153 -B:235

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:24 -Pro A:25
2Trp A:52 -Pro A:53
3Ile B:24 -Pro B:25
4Trp B:52 -Pro B:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010255A129RCATZ_HUMANUnclassified  ---A/BA68R
2UniProtVAR_033719A286TCATZ_HUMANPolymorphism34069356A/BA225T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010255A129RCATZ_HUMANUnclassified  ---AA68R
2UniProtVAR_033719A286TCATZ_HUMANPolymorphism34069356AA225T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010255A129RCATZ_HUMANUnclassified  ---BA68R
2UniProtVAR_033719A286TCATZ_HUMANPolymorphism34069356BA225T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010255A129RCATZ_HUMANUnclassified  ---A/BA68R
2UniProtVAR_033719A286TCATZ_HUMANPolymorphism34069356A/BA225T

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATZ_HUMAN256-275
 
  2A:195-214
B:195-214
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATZ_HUMAN256-275
 
  1A:195-214
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATZ_HUMAN256-275
 
  1-
B:195-214
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATZ_HUMAN256-275
 
  2A:195-214
B:195-214

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002171311aENSE00001454208chr20:57582302-57582041262CATZ_HUMAN1-48480--
1.2aENST000002171312aENSE00000663006chr20:57581540-57581377164CATZ_HUMAN48-103562A:1-42
B:1-42
42
42
1.3ENST000002171313ENSE00000663005chr20:57576699-57576520180CATZ_HUMAN103-163612A:42-102
B:42-102
61
61
1.4aENST000002171314aENSE00000663004chr20:57572808-57572658151CATZ_HUMAN163-213512A:102-152
B:102-152
51
51
1.5ENST000002171315ENSE00000663003chr20:57571856-57571694163CATZ_HUMAN213-267552A:152-206
B:152-206
55
55
1.6ENST000002171316ENSE00000845864chr20:57570814-57570240575CATZ_HUMAN268-303362A:207-242
B:207-242
36
36

(-) 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:242
 aligned with CATZ_HUMAN | Q9UBR2 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:242
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  
           CATZ_HUMAN    62 LPKSWDWRNVDGVNYASITRNQHIPQYCGSCWAHASTSAMADRINIKRKGAWPSTLLSVQNVIDCGNAGSCEGGNDLSVWDYAHQHGIPDETCNNYQAKDQECDKFNQCGTCNEFKECHAIRNYTLWRVGDYGSLSGREKMMAEIYANGPISCGIMATERLANYTGGIYAEYQDTTYINHVVSVAGWGISDGTEYWIVRNSWGEPWGERGWLRIVTSTYKDGKGARYNLAIEEHCTFGDPIV 303
               SCOP domains d1ef7a_ A: (Pro)cathepsin X                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ef7A00 A:1-242 Cysteine proteinases                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.......................hhhhhhhhhhhhhhhhhhh.........hhhhhhhhh..ee..eehhhhhhhhhhhh.ee.hhhh.........hhhhhhee.......ee.....eeeeeeeeee.hhhhhhhhhhhhh.eeeee..hhhhhh....ee..........eeeeeeeeee....eeeeee...........eeeee......hhhhhh..hhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------T----------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTEASE_ASN  ---------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-42 UniProt: 48-103    -----------------------------------------------------------Exon 1.4a  PDB: A:102-152 UniProt: 163-213         ------------------------------------------------------Exon 1.6  PDB: A:207-242             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3  PDB: A:42-102 UniProt: 103-163                     -------------------------------------------------Exon 1.5  PDB: A:152-206 UniProt: 213-267              ------------------------------------ Transcript 1 (2)
                 1ef7 A   1 LPKSWDWRNVDGVNYASITRNQHIPQYCGSCWAHASTSAMADRINIKRKGAWPSTLLSVQNVIDCGNAGSCEGGNDLSVWDYAHQHGIPDETCNNYQAKDQECDKFNQCGTCNEFKECHAIRNYTLWRVGDYGSLSGREKMMAEIYANGPISCGIMATERLANYTGGIYAEYQDTTYINHVVSVAGWGISDGTEYWIVRNSWGEPWGERGWLRIVTSTYKDGKGARYNLAIEEHCTFGDPIV 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with CATZ_HUMAN | Q9UBR2 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:242
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  
           CATZ_HUMAN    62 LPKSWDWRNVDGVNYASITRNQHIPQYCGSCWAHASTSAMADRINIKRKGAWPSTLLSVQNVIDCGNAGSCEGGNDLSVWDYAHQHGIPDETCNNYQAKDQECDKFNQCGTCNEFKECHAIRNYTLWRVGDYGSLSGREKMMAEIYANGPISCGIMATERLANYTGGIYAEYQDTTYINHVVSVAGWGISDGTEYWIVRNSWGEPWGERGWLRIVTSTYKDGKGARYNLAIEEHCTFGDPIV 303
               SCOP domains d1ef7b_ B: (Pro)cathepsin X                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ef7B00 B:1-242 Cysteine proteinases                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.......................hhhhhhhhhhhhhhhhhhh.........hhhhhhhhh..ee..eehhhhhhhhhhhh....hhhh.........hhhhhhee.......ee........eeeeeee.hhhhhhhhhhhhh.eeeee..hhhhhh....ee..........eeeeeeeeee....eeeeee...........eeeee..hhhhhhhhhh.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------T----------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTEASE_ASN  ---------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:1-42 UniProt: 48-103    -----------------------------------------------------------Exon 1.4a  PDB: B:102-152 UniProt: 163-213         ------------------------------------------------------Exon 1.6  PDB: B:207-242             Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3  PDB: B:42-102 UniProt: 103-163                     -------------------------------------------------Exon 1.5  PDB: B:152-206 UniProt: 213-267              ------------------------------------ Transcript 1 (2)
                 1ef7 B   1 LPKSWDWRNVDGVNYASITRNQHIPQYCGSCWAHASTSAMADRINIKRKGAWPSTLLSVQNVIDCGNAGSCEGGNDLSVWDYAHQHGIPDETCNNYQAKDQECDKFNQCGTCNEFKECHAIRNYTLWRVGDYGSLSGREKMMAEIYANGPISCGIMATERLANYTGGIYAEYQDTTYINHVVSVAGWGISDGTEYWIVRNSWGEPWGERGWLRIVTSTYKDGKGARYNLAIEEHCTFGDPIV 242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  

   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EF7)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CATZ_HUMAN | Q9UBR2)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-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: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: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:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0002003    angiotensin maturation    The process leading to the attainment of the full functional capacity of angiotensin by conversion of renin substrate into mature angiotensin in the blood.
    GO:0060441    epithelial tube branching involved in lung morphogenesis    The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
    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.
cellular component
    GO:0030134    COPII-coated ER to Golgi transport vesicle    A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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: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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        CATZ_HUMAN | Q9UBR21deu

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