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(-) Description

Title :  CRYSTAL STRUCTURE OF ATP-DEPENDENT PHOSPHOENOLPYRUVATE CARBOXYKINASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Sugahara, M. Miyano, N. Kunishima, Riken Structural Genomics/Pr Initiative (Rsgi)
Date :  21 Jan 03  (Deposition) - 11 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoenolpyruvate Carboxykinase, Adenosine Triphosphate, Thermus Thermophilus, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sugahara, N. Ohshima, Y. Ukita, M. Sugahara, N. Kunishima
Structure Of Atp-Dependent Phosphoenolpyruvate Carboxykinas From Thermus Thermophilus Hb8 Showing The Structural Basis Of Induced Fit And Thermostability.
Acta Crystallogr. , Sect. D V. 61 1500 2005
PubMed-ID: 16239727  |  Reference-DOI: 10.1107/S090744490502651X

(-) Compounds

Molecule 1 - ATP-DEPENDENT PHOSPHOENOLPYRUVATE CARBOXYKINASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3PO49Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:130 , ASN A:131 , PHE A:133 , GLY A:267 , HOH A:3030BINDING SITE FOR RESIDUE CA A 1001
02AC2SOFTWAREARG B:130 , ASN B:131 , PHE B:133 , GLY B:267 , HOH B:3104BINDING SITE FOR RESIDUE CA B 1002
03AC3SOFTWAREVAL A:20 , SER A:21 , ARG A:130 , ARG A:137 , HOH A:3016 , HOH A:3020 , HOH A:3028 , HIS B:38BINDING SITE FOR RESIDUE PO4 A 2001
04AC4SOFTWARELYS A:413 , LYS A:416 , HIS A:417 , HOH A:3145BINDING SITE FOR RESIDUE PO4 A 2002
05AC5SOFTWARELEU A:233 , SER A:234 , GLY A:235 , THR A:236 , GLY A:237 , LYS A:238 , THR A:239 , LYS A:272 , HOH A:3176 , HOH A:3286BINDING SITE FOR RESIDUE PO4 A 2003
06AC6SOFTWAREARG A:340 , HOH A:3045 , HOH A:3190BINDING SITE FOR RESIDUE PO4 A 2004
07AC7SOFTWAREHIS A:38 , HOH A:3040 , HOH A:3052 , HOH A:3127 , SER B:21 , PRO B:22 , ARG B:130 , ARG B:137 , HOH B:3261BINDING SITE FOR RESIDUE PO4 B 2005
08AC8SOFTWAREGLU B:259 , LYS B:413 , LYS B:416 , HIS B:417 , HOH B:3310BINDING SITE FOR RESIDUE PO4 B 2006
09AC9SOFTWARELEU B:233 , SER B:234 , GLY B:235 , THR B:236 , GLY B:237 , LYS B:238 , THR B:239 , HOH B:3178 , HOH B:3184 , HOH B:3246 , HOH B:3248BINDING SITE FOR RESIDUE PO4 B 2007
10BC1SOFTWAREGLU B:5 , HIS B:10 , LYS B:12 , HOH B:3314BINDING SITE FOR RESIDUE PO4 B 2008
11BC2SOFTWAREARG B:111 , ARG B:210BINDING SITE FOR RESIDUE PO4 B 2009
12BC3SOFTWARETYR A:93 , GLN A:161 , ARG A:166 , HOH A:3164BINDING SITE FOR RESIDUE GOL A 3001
13BC4SOFTWAREPHE B:160 , GLN B:161 , ARG B:166 , HOH B:3097 , HOH B:3243BINDING SITE FOR RESIDUE GOL B 3002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J3B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:47 -Pro A:48
2Thr B:47 -Pro B:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J3B)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_ATPPS00532 Phosphoenolpyruvate carboxykinase (ATP) signature.PCKA_THET8249-264
 
  2A:249-264
B:249-264

(-) Exons   (0, 0)

(no "Exon" information available for 1J3B)

(-) 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:513
 aligned with PCKA_THET8 | Q5SLL5 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:528
                                    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       401       411       421       431       441       451       461       471       481       491       501       511       521        
           PCKA_THET8     2 QRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTESPWHALFARNMFILPRRFGNDDEVEAFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTLSTDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSPEEAMYYFLSGYTARVAGTERGVTEPRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETWADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRTE 529
               SCOP domains d1j3ba2 A:2-211 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                          d1j3ba1 A:212-529 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1j3bA01 A:2-33,A:55-211         1j3bA02          ----1j3bA01 A:2-33,A:55-211 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                          1j3bA03 A:212-267,A:330-526                             1j3bA02 A:34-50,A:268-327                                   --1j3bA03 A:212-267,A:330-526  [code=3.90.228.20,          no name defined]                                                                                                                            --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh......eee..hhhhhhhhhhhh...ee.....eee........hhh.eeee...............eeehhhhhhhhhhhhhhhhhh..eeeeeeee.......eeeeeee.hhhhhhhhhhhh.hhhhhh------.....eeeeee.....hhhhhh.....eeeee....eeeee....hhhhhhhhhhhhhhhhhhhh.eeee.eeee.....eeeeee....hhhhhh......eee..eeee....eee...eeeee........hhhhhhhhh....eee..ee......ee..........eeeee.hhh.......ee..eeeeeeee.........eeeehhhhhhhhhhhheeee.---------.eeee.hhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeee..ee.......ee.hhhhhhhhhhhhhhhhhhhh.eee......eee......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_ATP       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j3b A   2 QRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTESPWHALFARNMFILPRRFG------AFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTLSTDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSPEEAMYYFLSGYTARV---------PRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETWADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRTE 529
                                    11        21        31        41        51        61        71        81        91       101       111       121       131        |-     | 151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371    |    -    |  391       401       411       421       431       441       451       461       471       481       491       501       511       521        
                                                                                                                                                                    140    147                                                                                                                                                                                                                                  376       386                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:518
 aligned with PCKA_THET8 | Q5SLL5 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:527
                                    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       401       411       421       431       441       451       461       471       481       491       501       511       521       
           PCKA_THET8     2 QRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTESPWHALFARNMFILPRRFGNDDEVEAFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTLSTDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSPEEAMYYFLSGYTARVAGTERGVTEPRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETWADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRT 528
               SCOP domains d1j3bb2 B:2-211 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                          d1j3bb1 B:212-528 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1j3bB01 B:2-33,B:55-211         1j3bB02          ----1j3bB01 B:2-33,B:55-211 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                          1j3bB03 B:212-267,B:330-526                             1j3bB02 B:34-50,B:268-327                                   --1j3bB03 B:212-267,B:330-526  [code=3.90.228.20,          no name defined]                                                                                                                            -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......eee..hhhhhhhhhhhh...ee.....eee........hhh.eeee...............eeehhhhhhhhhhhhhhhhhh..eeeeeeee.......eeeeeee.hhhhhhhhhhhh.hhhhhh...........eeeeee.....hhhhhh.....eeeee....eeeee....hhhhhhhhhhhhhhhhhhh..eeee.eeee.....eeeeee....hhhhhhh.....eee..eeee....eee...eeeee........hhhhhhhhh....eee..ee......ee..........eeeee.hhh.......ee..eeeeeeee.........eee.hhhhhhhhhhhheeee.---------.eeee.hhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeee..ee.......ee.hhhhhhhhhhhhhhhhhhhh.eee......eee......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_ATP       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j3b B   2 QRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTESPWHALFARNMFILPRRFGNDDEVEAFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTLSTDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSPEEAMYYFLSGYTARV---------PRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETWADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRT 528
                                    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    |    -    |  391       401       411       421       431       441       451       461       471       481       491       501       511       521       
                                                                                                                                                                                                                                                                                                                                                                                                                376       386                                                                                                                                              

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J3B)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PCKA_THET8 | Q5SLL5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004612    phosphoenolpyruvate carboxykinase (ATP) activity    Catalysis of the reaction: ATP + oxaloacetate = ADP + CO(2) + H(+) + phosphoenolpyruvate.
    GO:0004611    phosphoenolpyruvate carboxykinase activity    Catalysis of the reaction: source of phosphate + oxaloacetate = phosphoenolpyruvate + CO2 + other reaction products.
    GO:0017076    purine nucleotide binding    Interacting selectively and non-covalently with purine nucleotides, any compound consisting of a purine nucleoside esterified with (ortho)phosphate.
biological process
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCKA_THET8 | Q5SLL51xkv 2pc9

(-) Related Entries Specified in the PDB File

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