Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH BETA-SULFOPYRUVATE AND GTP
 
Authors :  S. M. Sullivan, T. Holyoak
Date :  14 Jul 08  (Deposition) - 26 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Kinase, Gluconeogenesis, Lyase, Decarboxylase, Gtp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. M. Sullivan, T. Holyoak
Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead Of Conformational Selection.
Proc. Natl. Acad. Sci. Usa V. 105 13829 2008
PubMed-ID: 18772387  |  Reference-DOI: 10.1073/PNAS.0805364105

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]
    ChainsA, B
    EC Number4.1.1.32
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T2
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePCK1
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPEPCK-C, PHOSPHOENOLPYRUVATE CARBOXYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ETX2Ligand/Ion2-ETHOXYETHANOL
3GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
4MN5Ligand/IonMANGANESE (II) ION
5NA2Ligand/IonSODIUM ION
6SPV2Ligand/IonSULFOPYRUVATE
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ETX1Ligand/Ion2-ETHOXYETHANOL
3GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
4MN-1Ligand/IonMANGANESE (II) ION
5NA-1Ligand/IonSODIUM ION
6SPV1Ligand/IonSULFOPYRUVATE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2ETX1Ligand/Ion2-ETHOXYETHANOL
3GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
4MN-1Ligand/IonMANGANESE (II) ION
5NA-1Ligand/IonSODIUM ION
6SPV1Ligand/IonSULFOPYRUVATE
Biological Unit 3 (4, 7)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ETX2Ligand/Ion2-ETHOXYETHANOL
3GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
4MN-1Ligand/IonMANGANESE (II) ION
5NA-1Ligand/IonSODIUM ION
6SPV2Ligand/IonSULFOPYRUVATE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:244 , HIS A:264 , ASP A:311BINDING SITE FOR RESIDUE MN A 700
02AC2SOFTWARETHR A:291 , ASP A:310BINDING SITE FOR RESIDUE MN A 701
03AC3SOFTWARETHR A:291BINDING SITE FOR RESIDUE MN A 703
04AC4SOFTWARELEU A:79 , ASN A:208BINDING SITE FOR RESIDUE NA A 1100
05AC5SOFTWARELYS B:244 , HIS B:264 , ASP B:311BINDING SITE FOR RESIDUE MN B 700
06AC6SOFTWARETHR B:291BINDING SITE FOR RESIDUE MN B 701
07AC7SOFTWARELEU B:79 , ASN B:208BINDING SITE FOR RESIDUE NA B 1100
08AC8SOFTWAREHIS A:264 , PRO A:285 , SER A:286 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , ASP A:311 , PRO A:337 , ARG A:405 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533BINDING SITE FOR RESIDUE GTP A 800
09AC9SOFTWAREARG A:87 , GLY A:237 , LYS A:243 , LYS A:244 , HIS A:264 , SER A:286 , ASP A:311 , PHE A:333 , ARG A:405 , ALA A:467BINDING SITE FOR RESIDUE SPV A 900
10BC1SOFTWARETRP A:260 , LYS A:316 , ARG A:324 , GLU A:424BINDING SITE FOR RESIDUE 1PE A 1000
11BC2SOFTWAREHIS B:264 , PRO B:285 , SER B:286 , ALA B:287 , CYS B:288 , GLY B:289 , LYS B:290 , THR B:291 , ASN B:292 , ASP B:311 , ARG B:405 , ARG B:436 , TRP B:516 , PHE B:517 , PHE B:525 , GLY B:529 , PHE B:530 , ASN B:533BINDING SITE FOR RESIDUE GTP B 800
12BC3SOFTWAREARG B:87 , GLY B:237 , LYS B:243 , LYS B:244 , HIS B:264 , SER B:286 , ASP B:311 , PHE B:333 , ARG B:405BINDING SITE FOR RESIDUE SPV B 900
13BC4SOFTWAREGLU B:446 , ALA B:447 , SER B:449 , LEU B:508 , PRO B:509 , LYS B:510 , ILE B:511BINDING SITE FOR RESIDUE ETX B 3430
14BC5SOFTWAREALA A:447 , SER A:449 , LEU A:508 , PRO A:509 , LYS A:510 , ILE A:511BINDING SITE FOR RESIDUE ETX A 3430

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DT7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:200 -Pro A:201
2Asn B:7 -Gly B:8
3Leu B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DT7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_GTPPS00505 Phosphoenolpyruvate carboxykinase (GTP) signature.PCKGC_RAT284-292
 
  2A:284-292
B:284-292
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_GTPPS00505 Phosphoenolpyruvate carboxykinase (GTP) signature.PCKGC_RAT284-292
 
  1A:284-292
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_GTPPS00505 Phosphoenolpyruvate carboxykinase (GTP) signature.PCKGC_RAT284-292
 
  1-
B:284-292
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_GTPPS00505 Phosphoenolpyruvate carboxykinase (GTP) signature.PCKGC_RAT284-292
 
  2A:284-292
B:284-292

(-) Exons   (9, 18)

Asymmetric Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000315861ENSRNOE00000330605chr3:164012410-164012511102PCKGC_RAT-00--
1.2ENSRNOT000000315862ENSRNOE00000271129chr3:164012684-164012948265PCKGC_RAT1-75752A:1-75
B:4-75
75
72
1.3ENSRNOT000000315863ENSRNOE00000271110chr3:164013321-164013502182PCKGC_RAT75-136622A:75-136
B:75-136
62
62
1.4ENSRNOT000000315864ENSRNOE00000271108chr3:164014063-164014266204PCKGC_RAT136-204692A:136-204
B:136-204
69
69
1.5ENSRNOT000000315865ENSRNOE00000271105chr3:164014535-164014722188PCKGC_RAT204-266632A:204-266
B:204-266
63
63
1.6ENSRNOT000000315866ENSRNOE00000271102chr3:164015301-164015463163PCKGC_RAT267-321552A:267-321
B:267-321
55
55
1.7ENSRNOT000000315867ENSRNOE00000271098chr3:164016073-164016297225PCKGC_RAT321-396762A:321-396
B:321-396
76
76
1.8ENSRNOT000000315868ENSRNOE00000271095chr3:164016388-164016519132PCKGC_RAT396-440452A:396-440
B:396-440
45
45
1.9ENSRNOT000000315869ENSRNOE00000271092chr3:164017053-16401714896PCKGC_RAT440-472332A:440-472
B:440-464
33
25
1.10ENSRNOT0000003158610ENSRNOE00000271120chr3:164017282-1640183451064PCKGC_RAT472-6221512A:472-622
B:473-622
151
150

(-) 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:624
 aligned with PCKGC_RAT | P07379 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:624
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        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       488       498       508       518       528       538       548       558       568       578       588       598       608       618    
            PCKGC_RAT     - --MPPQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
               SCOP domains d3dt7a1 A:-1-259 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                       d3dt7a2 A:260-622 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------3dt7A01 A:11-64,A:88-259                              3dt7A02                3dt7A01 A:11-64,A:88-259 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                                        3dt7A03 A:260-329,A:415-622  [code=3.90.228.20, no name defined]      3dt7A02 A:65-87,A:330-414 Phosphoenolpyruvate Carboxykinase, domain 2                3dt7A03 A:260-329,A:415-622  [code=3.90.228.20, no name defined]                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhh.eee.hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...ee.......eee.........hhh.eeee..hhhhhh............eehhhhhhhhhhh.........eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhhhhh....eeeeee.................hhhhheeeee....eeeee...hhhhhh.......hhhhhhhhhhhh.eee..eeeeee.....eeeeeee.....hhhhhhh........eeeeee...eeeee.....eeee....eeeee........hhhhhhhh....eee..eee....ee.............ee.....ee.............eeeee.hhh............eeeeeeeee.........eee..hhhhhhhhhhh.eee...........eee.hhhh......hhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhhhhhhh....eeee..eeee.............hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_GTP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) --Exon 1.2  PDB: A:1-75 UniProt: 1-75                                        ------------------------------------------------------------Exon 1.4  PDB: A:136-204 UniProt: 136-204                            --------------------------------------------------------------Exon 1.6  PDB: A:267-321 UniProt: 267-321              --------------------------------------------------------------------------Exon 1.8  PDB: A:396-440 UniProt: 396-440    -------------------------------Exon 1.10  PDB: A:472-622 UniProt: 472-622                                                                                                              Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.3  PDB: A:75-136 UniProt: 75-136                       -------------------------------------------------------------------Exon 1.5  PDB: A:204-266 UniProt: 204-266                      ------------------------------------------------------Exon 1.7  PDB: A:321-396 UniProt: 321-396                                   -------------------------------------------Exon 1.9  PDB: A:440-472         ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3dt7 A  -1 GSMPPQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                     8        18        28        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       488       498       508       518       528       538       548       558       568       578       588       598       608       618    

Chain B from PDB  Type:PROTEIN  Length:611
 aligned with PCKGC_RAT | P07379 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:619
                                    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       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613         
            PCKGC_RAT     4 QLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
               SCOP domains d3dt7b1 B:4-259 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                   d3dt7b2 B:260-622 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------3dt7B01 B:11-64,B:88-259                              3dt7B02                3dt7B01 B:11-64,B:88-259 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                                        3dt7B03 B:260-329,B:415-622  [code=3.90.228.20, no name defined]      3dt7B02 B:65-87,B:330-414 Phosphoenolpyruvate Carboxykinase, domain 2                3dt7B03 B:260-329,B:415-622  [code=3.90.228.20, no         name defined]                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eee.hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...ee.......eee.........hhh.eeee..hhhhhh............eehhhhhhhhhhh.........eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhhhhh....eeeeee.................hhhhheeeeehhh.eeeee...hhhhhh.......hhhhhhhhhhhh.eee..eeeeee.....eeeeeee.....hhhhhhh........eeeeee...eeeee.....eeee....eeeee........hhhhhhhh....eee..eee....ee.............ee.....ee.............eeeee.hhh............eeeeeeeee.........eee..hhhhhhhhhhh.eee.--------..eee.hhhh......hhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhhhhhhh....eeee..eeee.............hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_GTP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:4-75 UniProt: 1-75 [INCOMPLETE]                        ------------------------------------------------------------Exon 1.4  PDB: B:136-204 UniProt: 136-204                            --------------------------------------------------------------Exon 1.6  PDB: B:267-321 UniProt: 267-321              --------------------------------------------------------------------------Exon 1.8  PDB: B:396-440 UniProt: 396-440    -------------------------------Exon 1.10  PDB: B:473-622 UniProt: 472-622 [INCOMPLETE]                                                                                                 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.3  PDB: B:75-136 UniProt: 75-136                       -------------------------------------------------------------------Exon 1.5  PDB: B:204-266 UniProt: 204-266                      ------------------------------------------------------Exon 1.7  PDB: B:321-396 UniProt: 321-396                                   -------------------------------------------Exon 1.9  PDB: B:440-464         ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3dt7 B   4 QLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEA--------KVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    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       403       413       423       433       443       453       463|      473       483       493       503       513       523       533       543       553       563       573       583       593       603       613         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      464      473                                                                                                                                                     

   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 Unit

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DT7)

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PCKGC_RAT | P07379)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0031406    carboxylic acid binding    Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004550    nucleoside diphosphate kinase activity    Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
    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:0004613    phosphoenolpyruvate carboxykinase (GTP) activity    Catalysis of the reaction: GTP + oxaloacetate = GDP + phosphoenolpyruvate + CO2.
    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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0071320    cellular response to cAMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0071332    cellular response to fructose stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fructose stimulus.
    GO:0071377    cellular response to glucagon stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0071347    cellular response to interleukin-1    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0051365    cellular response to potassium ion starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of potassium ions.
    GO:0071300    cellular response to retinoic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0071356    cellular response to tumor necrosis factor    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    GO:0017144    drug metabolic process    The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0046327    glycerol biosynthetic process from pyruvate    The chemical reactions and pathways resulting in the formation of glycerol, 1,2,3-propanetriol, from other compounds, including pyruvate.
    GO:0006475    internal protein amino acid acetylation    The addition of an acetyl group to a non-terminal amino acid in a protein.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006165    nucleoside diphosphate phosphorylation    The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
    GO:0006107    oxaloacetate metabolic process    The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of the TCA cycle.
    GO:0061402    positive regulation of transcription from RNA polymerase II promoter in response to acidic pH    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH stimulus with pH < 7.
    GO:0014823    response to activity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an activity stimulus.
    GO:0032868    response to insulin    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0070741    response to interleukin-6    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-6 stimulus.
    GO:0033993    response to lipid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:1904640    response to methionine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methionine stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ETX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SPV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn B:7 - Gly B:8   [ RasMol ]  
    Leu A:200 - Pro A:201   [ RasMol ]  
    Leu B:200 - Pro B:201   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dt7
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PCKGC_RAT | P07379
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.32
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PCKGC_RAT | P07379
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PCKGC_RAT | P073792qew 2qey 2qf1 2qf2 2rk7 2rk8 2rka 2rkd 2rke 3dt2 3dt4 3dtb 3moe 3mof 3moh 4gmm 4gmu 4gmw 4gmz 4gnl 4gnm 4gno 4gnp 4gnq 4ox2 4yw8 4yw9 4ywb 4ywd 5fh0 5fh1 5fh2 5fh3 5fh4 5fh5 5v95 5v97 5v9f 5v9g 5v9h

(-) Related Entries Specified in the PDB File

3dt2 RAT CPEPCK IN COMPLEX WITH OXALATE AND GTP, COCRYSTAL
3dt4 COMPLEX WITH OXALATE AND GTP, OXALATE SOAKED INTO PEPCK-GTP
3dtb COMPLEX WITH PHOSPHOGLYCOLATE AND GTP