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(-) Description

Title :  CRYSTAL STRUCTURE OF CA2 SITE MUTANT OF PRO-S324A
 
Authors :  Y. Takeuchi, S. Tanaka, H. Matsumura, Y. Koga, K. Takano, S. Kanaya
Date :  17 Dec 08  (Deposition) - 23 Jun 09  (Release) - 28 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Subtilisin, Thermococcus Kodakaraensis, Calcium Ion, Calcium, Hydrolase, Protease, Secreted, Serine Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Takeuchi, S. Tanaka, H. Matsumura, Y. Koga, K. Takano, S. Kanaya
Requirement Of A Unique Ca(2+)-Binding Loop For Folding Of Tk-Subtilisin From A Hyperthermophilic Archaeon.
Biochemistry V. 48 10637 2009
PubMed-ID: 19813760  |  Reference-DOI: 10.1021/BI901334B

(-) Compounds

Molecule 1 - TK-SUBTILISIN
    ChainsA, B, C
    EC Number3.4.21.62
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET25B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificTHERMOCOCCUS KODAKARAENSIS
    Organism Taxid311400

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1CA16Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:84 , ASP A:124 , LEU A:164 , ASN A:166 , ILE A:168 , VAL A:170BINDING SITE FOR RESIDUE CA A 399
02AC2SOFTWAREASP A:212 , ASP A:214 , ASP A:216 , ILE A:218 , ASP A:222 , ASP A:225BINDING SITE FOR RESIDUE CA A 400
03AC3SOFTWAREASP A:214 , ASP A:216 , ASP A:222 , ASP A:224 , HOH A:607BINDING SITE FOR RESIDUE CA A 401
04AC4SOFTWAREVAL A:108 , GLN A:110 , ALA A:227 , GLU A:229 , HOH A:447 , HOH A:580BINDING SITE FOR RESIDUE CA A 402
05AC5SOFTWAREASP A:119 , ASP A:121 , ASP A:314 , ASP A:315 , HOH A:604BINDING SITE FOR RESIDUE CA A 403
06AC6SOFTWAREASP A:372 , LEU A:373 , PRO A:375 , GLY A:377 , ASP A:379 , HOH A:560BINDING SITE FOR RESIDUE CA A 404
07AC7SOFTWAREGLN B:84 , ASP B:124 , LEU B:164 , ASN B:166 , ILE B:168 , VAL B:170BINDING SITE FOR RESIDUE CA B 399
08AC8SOFTWAREASP B:212 , ASP B:214 , ASP B:216 , ILE B:218 , ASP B:222 , ASP B:225BINDING SITE FOR RESIDUE CA B 400
09AC9SOFTWARETHR A:142 , HOH A:438 , ASP B:214 , ASP B:216 , ASP B:222 , ASP B:224BINDING SITE FOR RESIDUE CA B 401
10BC1SOFTWAREASP B:372 , LEU B:373 , PRO B:375 , GLY B:377 , ASP B:379BINDING SITE FOR RESIDUE CA B 402
11BC2SOFTWAREVAL B:108 , GLN B:110 , ALA B:227 , GLU B:229 , HOH B:433 , HOH B:651BINDING SITE FOR RESIDUE CA B 403
12BC3SOFTWAREGLN C:84 , ASP C:124 , LEU C:164 , ASN C:166 , ILE C:168 , VAL C:170BINDING SITE FOR RESIDUE CA C 399
13BC4SOFTWAREASP C:212 , ASP C:214 , ASP C:216 , ILE C:218 , ASP C:222 , ASP C:225BINDING SITE FOR RESIDUE CA C 400
14BC5SOFTWAREASP C:214 , ASP C:216 , ASP C:222 , HOH C:533BINDING SITE FOR RESIDUE CA C 401
15BC6SOFTWAREASP C:372 , LEU C:373 , PRO C:375 , GLY C:377 , ASP C:379 , HOH C:486BINDING SITE FOR RESIDUE CA C 402
16BC7SOFTWAREVAL C:108 , GLN C:110 , ALA C:227 , GLU C:229 , HOH C:521 , HOH C:544BINDING SITE FOR RESIDUE CA C 403

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:132 -A:147
2B:132 -B:147
3C:132 -C:147

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Tyr A:272 -Pro A:273
2Pro A:313 -Asp A:314
3Tyr B:272 -Pro B:273
4Pro B:313 -Asp B:314
5Tyr C:272 -Pro C:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.TKSU_THEKO135-146
 
 
  3A:111-122
B:111-122
C:111-122
2SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.TKSU_THEKO346-356
 
 
  3A:322-332
B:322-332
C:322-332
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.TKSU_THEKO135-146
 
 
  1A:111-122
-
-
2SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.TKSU_THEKO346-356
 
 
  1A:322-332
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.TKSU_THEKO135-146
 
 
  1-
B:111-122
-
2SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.TKSU_THEKO346-356
 
 
  1-
B:322-332
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.TKSU_THEKO135-146
 
 
  1-
-
C:111-122
2SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.TKSU_THEKO346-356
 
 
  1-
-
C:322-332

(-) Exons   (0, 0)

(no "Exon" information available for 2ZWO)

(-) 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:395
 aligned with TKSU_THEKO | P58502 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:395
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417     
           TKSU_THEKO    28 NTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLLGKPSWLGGGSTQPAQTIPWGIERVKAPSVWSITDGSVSVIQVAVLDTGVDYDHPDLAANIAWCVSTLRGKVSTKLRDCADQNGHGTHVIGTIAALNNDIGVVGVAPGVQIYSVRVLDARGSGSYSDIAIGIEQAILGPDGVADKDGDGIIAGDPDDDAAEVISMSLGGPADDSYLYDMIIQAYNAGIVIVAASGNEGAPSPSYPAAYPEVIAVGAIDSNDNIASFSNRQPEVSAPGVDILSTYPDDSYETLMGTSMATPHVSGVVALIQAAYYQKYGKILPVGTFDDISKNTVRGILHITADDLGPTGWDADYGYGVVRAALAVQAALG 422
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee......hhhhhhh..eeeee.....eeeeeee..hhhhhhh...eeeeee..eeee..ee............eehhhhhhh.hhhhhhh........eeeeee.........hhh.eeeeee.hhhh...hhhhhh...hhhhhhhhhhhh..............eeeeee......eeehhhhhhhhhhhhhhhhh....................eeee.ee....hhhhhhhhhhhhhh..eeeee.................eeeeeee...............eeee...eeeee...eeeeeehhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhh.................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------SUBTILASE_AS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zwo A   4 NTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLLGKPSWLGGGSTQPAQTIPWGIERVKAPSVWSITDGSVSVIQVAVLDTGVDYDHPDLAANIAWCVSTLRGKVSTKLRDCADQNGHGTHVIGTIAALNNDIGVVGVAPGVQIYSVRVLDARGSGSYSDIAIGIEQAILGPDGVADKDGDGIIAGDPDDAAAEVISMSLGGPADDSYLYDMIIQAYNAGIVIVAASGNEGAPSPSYPAAYPEVIAVGAIDSNDNIASFSNRQPEVSAPGVDILSTYPDDSYETLMGTAMATPHVSGVVALIQAAYYQKYGKILPVGTFDDISKNTVRGILHITADDLGPTGWDADYGYGVVRAALAVQAALG 398
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     

Chain B from PDB  Type:PROTEIN  Length:393
 aligned with TKSU_THEKO | P58502 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:397
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       
           TKSU_THEKO    26 EQNTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLLGKPSWLGGGSTQPAQTIPWGIERVKAPSVWSITDGSVSVIQVAVLDTGVDYDHPDLAANIAWCVSTLRGKVSTKLRDCADQNGHGTHVIGTIAALNNDIGVVGVAPGVQIYSVRVLDARGSGSYSDIAIGIEQAILGPDGVADKDGDGIIAGDPDDDAAEVISMSLGGPADDSYLYDMIIQAYNAGIVIVAASGNEGAPSPSYPAAYPEVIAVGAIDSNDNIASFSNRQPEVSAPGVDILSTYPDDSYETLMGTSMATPHVSGVVALIQAAYYQKYGKILPVGTFDDISKNTVRGILHITADDLGPTGWDADYGYGVVRAALAVQAALG 422
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhh..eeeee.....eeeeeee..hhhhhh....eeeeee..eeee..ee..----........hhhhhhh...hhhhh........eeeeee.........hhh.eeeeee.hhhh...hhhhhh...hhhhhhhhhhhh..............eeeeee......eeehhhhhhhhhhhhhh.......................eeee.ee....hhhhhhhhhhhhhh..eeeee.................eeeeeee...............eeee...eeeee...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhh.................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------SUBTILASE_AS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zwo B   2 EQNTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLLGKPSW----STQPAQTIPWGIERVKAPSVWSITDGSVSVIQVAVLDTGVDYDHPDLAANIAWCVSTLRGKVSTKLRDCADQNGHGTHVIGTIAALNNDIGVVGVAPGVQIYSVRVLDARGSGSYSDIAIGIEQAILGPDGVADKDGDGIIAGDPDDAAAEVISMSLGGPADDSYLYDMIIQAYNAGIVIVAASGNEGAPSPSYPAAYPEVIAVGAIDSNDNIASFSNRQPEVSAPGVDILSTYPDDSYETLMGTAMATPHVSGVVALIQAAYYQKYGKILPVGTFDDISKNTVRGILHITADDLGPTGWDADYGYGVVRAALAVQAALG 398
                                    11        21        31        41        51        61        71  |    |81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       
                                                                                                   74   79                                                                                                                                                                                                                                                                                                                               

Chain C from PDB  Type:PROTEIN  Length:389
 aligned with TKSU_THEKO | P58502 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:395
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417     
           TKSU_THEKO    28 NTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLLGKPSWLGGGSTQPAQTIPWGIERVKAPSVWSITDGSVSVIQVAVLDTGVDYDHPDLAANIAWCVSTLRGKVSTKLRDCADQNGHGTHVIGTIAALNNDIGVVGVAPGVQIYSVRVLDARGSGSYSDIAIGIEQAILGPDGVADKDGDGIIAGDPDDDAAEVISMSLGGPADDSYLYDMIIQAYNAGIVIVAASGNEGAPSPSYPAAYPEVIAVGAIDSNDNIASFSNRQPEVSAPGVDILSTYPDDSYETLMGTSMATPHVSGVVALIQAAYYQKYGKILPVGTFDDISKNTVRGILHITADDLGPTGWDADYGYGVVRAALAVQAALG 422
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhh..eeeee.....eeeeeee..hhhhhhhh..eeeeee..eeee..ee..------......hhhhhhh.hhhhh..........eeeeee.........hhh.eeeeee.hhhh...hhhhhh...hhhhhhhhhhhh..............eeeeee......eeehhhhhhhhhhhhhhhhh....................eeee.ee....hhhhhhhhhhhhhh..eeeee.................eeeeeee...............eeee...eeeee...eeeeeehhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhh.................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------SUBTILASE_AS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zwo C   4 NTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLLGKPSW------QPAQTIPWGIERVKAPSVWSITDGSVSVIQVAVLDTGVDYDHPDLAANIAWCVSTLRGKVSTKLRDCADQNGHGTHVIGTIAALNNDIGVVGVAPGVQIYSVRVLDARGSGSYSDIAIGIEQAILGPDGVADKDGDGIIAGDPDDAAAEVISMSLGGPADDSYLYDMIIQAYNAGIVIVAASGNEGAPSPSYPAAYPEVIAVGAIDSNDNIASFSNRQPEVSAPGVDILSTYPDDSYETLMGTAMATPHVSGVVALIQAAYYQKYGKILPVGTFDDISKNTVRGILHITADDLGPTGWDADYGYGVVRAALAVQAALG 398
                                    13        23        33        43        53        63        73|      |83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     
                                                                                                 74     81                                                                                                                                                                                                                                                                                                                             

   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 2ZWO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZWO)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (TKSU_THEKO | P58502)
molecular function
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in 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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  2zwo
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 Related Entries

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

UniProtKB/Swiss-Prot
        TKSU_THEKO | P585022e1p 2z2x 2z2y 2z2z 2z30 2z56 2z57 2z58 2zrq 2zwp 3a3n 3a3o 3a3p 3vhq 3vv2 3wiu 3wiv 4jp8

(-) Related Entries Specified in the PDB File

2e1p CRYSTAL STRUCTURE OF UNAUTOPROCESSED FORM2 OF TK-SUBTILISIN
2zwp