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

(-) Description

Title :  CRYSTAL STRUCTURE OF PREDICTED NUCLEOTIDE-BINDING PROTEIN FROM VIBRIO CHOLERAE
 
Authors :  Y. Patskovsky, C. Zhan, W. Shi, R. Toro, J. M. Sauder, J. Gilmore, M. Iizu M. Maletic, T. Gheyi, S. R. Wasserman, D. Smith, S. K. Burley, S. C. Almo Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  20 Apr 07  (Deposition) - 08 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, New York Structural Genomics Research Consortium, Nysgrc, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, C. Zhan, W. Shi, J. M. Sauder, J. Gilmore, M. Iizuka, M. Maletic, T. Gheyi, S. R. Wasserman, D. Smith, S. K. Burley, S. C. Almo
Crystal Structure Of Predicted Nucleotide-Binding Protein From Vibrio Cholerae.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Atcc: 39315
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: VC_0899
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: EL TOR INABA N16961
    Synonym: PREDICTED ROSSMANN FOLD NUCLEOTIDE-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 82)

Asymmetric/Biological Unit (3, 82)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE68Mod. Amino AcidSELENOMETHIONINE
3PO412Ligand/IonPHOSPHATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY D:158 , HIS D:159 , GLY D:260 , PRO D:261 , GLY D:262 , THR D:263 , HOH D:611 , HOH D:688 , HOH D:719 , HOH D:720BINDING SITE FOR RESIDUE PO4 D 601
02AC2SOFTWARELYS B:205 , GLU D:193 , LYS D:197 , ASN D:228BINDING SITE FOR RESIDUE PO4 D 602
03AC3SOFTWAREGLY B:158 , HIS B:159 , GLY B:260 , PRO B:261 , GLY B:262 , THR B:263 , HOH B:707 , HOH B:844BINDING SITE FOR RESIDUE PO4 B 603
04AC4SOFTWAREGLY A:158 , HIS A:159 , GLY A:260 , PRO A:261 , GLY A:262 , THR A:263 , HOH A:679 , HOH A:735BINDING SITE FOR RESIDUE PO4 A 604
05AC5SOFTWAREGLY C:158 , HIS C:159 , GLY C:260 , PRO C:261 , GLY C:262 , THR C:263 , HOH C:715 , HOH C:799BINDING SITE FOR RESIDUE PO4 C 605
06AC6SOFTWAREGLU A:74 , ARG A:75 , ARG D:339 , LYS D:343 , TYR D:349BINDING SITE FOR RESIDUE PO4 D 606
07AC7SOFTWAREPRO B:285 , ILE B:286 , HIS B:316 , TYR B:317 , SER B:318 , HOH B:841BINDING SITE FOR RESIDUE PO4 B 607
08AC8SOFTWARELYS A:205 , GLU C:193 , LYS C:197 , ASN C:228BINDING SITE FOR RESIDUE PO4 C 608
09AC9SOFTWAREARG B:339 , LYS B:343 , TYR B:349 , GLU C:74 , ARG C:75BINDING SITE FOR RESIDUE PO4 B 609
10BC1SOFTWAREARG A:339 , LYS A:343 , TYR A:349 , HOH C:771 , ARG D:75BINDING SITE FOR RESIDUE PO4 A 610
11BC2SOFTWAREARG B:75 , ARG C:339 , LYS C:343 , TYR C:349BINDING SITE FOR RESIDUE PO4 C 611
12BC3SOFTWAREGLU B:193 , LYS B:197 , ASN B:228 , LYS D:205BINDING SITE FOR RESIDUE PO4 B 612
13BC4SOFTWAREALA C:127 , THR C:131 , ARG C:249 , LEU C:355 , LYS C:356 , ILE C:357BINDING SITE FOR RESIDUE GOL C 701
14BC5SOFTWAREMSE B:16 , ASP B:17 , ARG B:107 , TYR B:111 , ASN B:140 , ARG C:139BINDING SITE FOR RESIDUE GOL B 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PMB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PMB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PMB)

(-) Exons   (0, 0)

(no "Exon" information available for 2PMB)

(-) 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:437
 aligned with Q9KTK3_VIBCH | Q9KTK3 from UniProtKB/TrEMBL  Length:457

    Alignment length:452
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454  
         Q9KTK3_VIBCH     5 TMIIQVSPAGSMDLLSQLEVERLKKTASSDLYQLYRNCSLAVLNSGSHTDNSKELLDKYKNFDITVMRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNMHLADSQRLNLTNATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAMEGPMKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVIMPDIEKRLEAFVRMAHGIIIFPGGPGTAEELLYILGIMMHPENADQPMPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARIMSNAMPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESMANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEMHGDPVLMKKMDQLLNDFVAQNRMKLPGGSAYEPCYKIV 456
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pmbA01   A:5-116 MoCo carrier protein-like                                                                              2pmbA02 A:126-455  [code=3.40.50.450, no name defined]                                                                                                                                                                                                                                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..--.....hhhhhhh.......hhhhhhhhhhhhhh..---.....hhhhhh...eeeeeee..eeeeeee..hhh.ee..eehhhhhhhhhhhhhhhhhhhh..---------hhhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh......eeeee...............eeee..hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhheeee.hhhhhhhhhhhhhhhhhhhhhhh............hhhhhh....hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhh.......-......eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pmb A   5 SLIIQVSP--SmDLLSQLEVERLKKTASSDLYQLYRNCSLAVLNS---TDNSKELLDKYKNFDITVmRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNmHL---------NATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAmEGPmKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVImPDIEKRLEAFVRmAHGIIIFPGGPGTAEELLYILGImmHPENADQPmPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARImSNAmPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESmANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEmHGDPVLmKKmDQLLNDFVAQNRmKLPG-SAYEPCYKIV 456
                                   | -||      24        34        44    |   54        64      | 74        84        94       104       114 |       - |     134       144       154       164       174       184       194 |     204       214       224       234  |    244     | 254       264       274|      284       294       304       314       324      |334|      344       354       364       374       384       394       404       414   |   424|  |   434      |444| |    454  
                                  12 15|                               49  53                71-MSE                                    114-MSE     126                                                               192-MSE                                      237-MSE      250-MSE                 274-MSE   284-MSE                                        331-MSE                                  372-MSE                                       418-MSE  |  |          441-MSE |         
                                      16-MSE                                                                                             116                                                                             196-MSE                                                                        275-MSE                                                     335-MSE                                                                                   425-MSE               447         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 428-MSE                        


Chain B from PDB  Type:PROTEIN  Length:437
 aligned with Q9KTK3_VIBCH | Q9KTK3 from UniProtKB/TrEMBL  Length:457

    Alignment length:452
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454  
         Q9KTK3_VIBCH     5 TMIIQVSPAGSMDLLSQLEVERLKKTASSDLYQLYRNCSLAVLNSGSHTDNSKELLDKYKNFDITVMRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNMHLADSQRLNLTNATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAMEGPMKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVIMPDIEKRLEAFVRMAHGIIIFPGGPGTAEELLYILGIMMHPENADQPMPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARIMSNAMPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESMANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEMHGDPVLMKKMDQLLNDFVAQNRMKLPGGSAYEPCYKIV 456
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pmbB01   B:5-116 MoCo car rier protein-like                                                                             2pmbB02 B:126-455  [code=3.40.50.450, no name defined]                                                                                                                                                                                                                                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..--.....hhhhhhhhh..-hhhhhhhhhhhhhhhh..---..............eeeeeee..eeeeeee..hhh.ee..eehhhhhhhhhhhhhhhhhhhhh.---------hhhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhh......eeeee...............eeee..hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhheeee.hhhhhhhhhhhhhhhhhhhhhhh............hhhhhh....hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhh..............eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pmb B   5 SLIIQVSP--SmDLLSQLEVERLKKT-SSDLYQLYRNCSLAVLNS---TDNSKELLDKYKNFDITVmRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNmHL---------NATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAmEGPmKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVImPDIEKRLEAFVRmAHGIIIFPGGPGTAEELLYILGImmHPENADQPmPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARImSNAmPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESmANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEmHGDPVLmKKmDQLLNDFVAQNRmKLPGGSAYEPCYKIV 456
                                   | -||      24     | |34        44    |   54        64      | 74        84        94       104       114 |       - |     134       144       154       164       174       184       194 |     204       214       224       234  |    244     | 254       264       274|      284       294       304       314       324      |334|      344       354       364       374       384       394       404       414   |   424|  |   434      |444       454  
                                  12 15|            30 |               49  53                71-MSE                                    114-MSE     126                                                               192-MSE                                      237-MSE      250-MSE                 274-MSE   284-MSE                                        331-MSE                                  372-MSE                                       418-MSE  |  |          441-MSE           
                                      16-MSE          32                                                                                 116                                                                             196-MSE                                                                        275-MSE                                                     335-MSE                                                                                   425-MSE                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 428-MSE                        


Chain C from PDB  Type:PROTEIN  Length:434
 aligned with Q9KTK3_VIBCH | Q9KTK3 from UniProtKB/TrEMBL  Length:457

    Alignment length:452
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454  
         Q9KTK3_VIBCH     5 TMIIQVSPAGSMDLLSQLEVERLKKTASSDLYQLYRNCSLAVLNSGSHTDNSKELLDKYKNFDITVMRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNMHLADSQRLNLTNATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAMEGPMKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVIMPDIEKRLEAFVRMAHGIIIFPGGPGTAEELLYILGIMMHPENADQPMPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARIMSNAMPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESMANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEMHGDPVLMKKMDQLLNDFVAQNRMKLPGGSAYEPCYKIV 456
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pmbC01   C:5-116 MoCo ca   rrier protein-like                                                                           2pmbC02 C:126-455  [code=3.40.50.450, no name defined]                                                                                                                                                                                                                                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..--.....hhhhhhhhh.---hhhhhhhhhhhhhhhh..----............eeeeeee..eeeeeee..hhh.ee..eehhhhhhhhhhhhhhhhhhhh..---------hhhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh......eeeee...............eeee..hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhheeee.hhhhhhhhhhhhhhhhhhhhhhh............hhhhhh....hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhh..............eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pmb C   5 SLIIQVSP--SmDLLSQLEVERLKK---SDLYQLYRNCSLAVLNSG----NSKELLDKYKNFDITVmRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNmHL---------NATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAmEGPmKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVImPDIEKRLEAFVRmAHGIIIFPGGPGTAEELLYILGImmHPENADQPmPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARImSNAmPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESmANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEmHGDPVLmKKmDQLLNDFVAQNRmKLPGGSAYEPCYKIV 456
                                   | -||      24    |   34        44     |   -|       64      | 74        84        94       104       114 |       - |     134       144       154       164       174       184       194 |     204       214       224       234  |    244     | 254       264       274|      284       294       304       314       324      |334|      344       354       364       374       384       394       404       414   |   424|  |   434      |444       454  
                                  12 15|           29  33               50   55              71-MSE                                    114-MSE     126                                                               192-MSE                                      237-MSE      250-MSE                 274-MSE   284-MSE                                        331-MSE                                  372-MSE                                       418-MSE  |  |          441-MSE           
                                      16-MSE                                                                                             116                                                                             196-MSE                                                                        275-MSE                                                     335-MSE                                                                                   425-MSE                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 428-MSE                        


Chain D from PDB  Type:PROTEIN  Length:437
 aligned with Q9KTK3_VIBCH | Q9KTK3 from UniProtKB/TrEMBL  Length:457

    Alignment length:452
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454  
         Q9KTK3_VIBCH     5 TMIIQVSPAGSMDLLSQLEVERLKKTASSDLYQLYRNCSLAVLNSGSHTDNSKELLDKYKNFDITVMRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNMHLADSQRLNLTNATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAMEGPMKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVIMPDIEKRLEAFVRMAHGIIIFPGGPGTAEELLYILGIMMHPENADQPMPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARIMSNAMPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESMANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEMHGDPVLMKKMDQLLNDFVAQNRMKLPGGSAYEPCYKIV 456
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pmbD01   D:5-117 MoCo car  rier protein-like                                                                            2pmbD02 D:126-455  [code=3.40.50.450, no name defined]                                                                                                                                                                                                                                                                                    - CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lysine_decarbox-2pmbD01 D:192-331                                                                                                           --DUF3412-2pmbD05 D:334-456                                                                                                   Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lysine_decarbox-2pmbD02 D:192-331                                                                                                           --DUF3412-2pmbD06 D:334-456                                                                                                   Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lysine_decarbox-2pmbD03 D:192-331                                                                                                           --DUF3412-2pmbD07 D:334-456                                                                                                   Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lysine_decarbox-2pmbD04 D:192-331                                                                                                           --DUF3412-2pmbD08 D:334-456                                                                                                   Pfam domains (4)
         Sec.struct. author ..eeee..--.....hhhhhhhhh..--hhhhhhhhhhhhhhhh.---......hhhhh...eeeeeee..eeeeeee..hhh.ee..eehhhhhhhhhhhhhhhhhhhh...--------hhhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh......eeeee...............eeee..hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhheeee.hhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh..............eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pmb D   5 SLIIQVSP--SmDLLSQLEVERLKKT--SDLYQLYRNCSLAVLNS---TDNSKELLDKYKNFDITVmRRERGIKLELANPPEHAFVDGQIIKGIQEHLFSVLRDIVYVNmHLA--------NATHITNLVFGILRNAGALIPGATPNLVVCWGGHSINEVEYQYTREVGHELGLRELNICTGCGPGAmEGPmKGAAVGHAKQRYSEYRYLGLTEPSIIAAEPPNPIVNELVImPDIEKRLEAFVRmAHGIIIFPGGPGTAEELLYILGImmHPENADQPmPIVLTGPKQSEAYFRSLDKFITDTLGEAARKHYSIAIDNPAEAARImSNAmPLVRQHRKDKEDAYSFNWSLKIEPEFQLPFEPNHESmANLDLHLNQRPEVLAANLRRAFSGVVAGNVKAEGIREIERHGPFEmHGDPVLmKKmDQLLNDFVAQNRmKLPGGSAYEPCYKIV 456
                                   | -||      24     |  34        44    |   54        64      | 74        84        94       104       114  |      - |     134       144       154       164       174       184       194 |     204       214       224       234  |    244     | 254       264       274|      284       294       304       314       324      |334|      344       354       364       374       384       394       404       414   |   424|  |   434      |444       454  
                                  12 15|            30 33              49  53                71-MSE                                    114-MSE     126                                                               192-MSE                                      237-MSE      250-MSE                 274-MSE   284-MSE                                        331-MSE                                  372-MSE                                       418-MSE  |  |          441-MSE           
                                      16-MSE                                                                                              117                                                                            196-MSE                                                                        275-MSE                                                     335-MSE                                                                                   425-MSE                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 428-MSE
   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 2PMB)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: DprA (10)
(-)
Clan: no clan defined [family: DUF3412] (1)
(-)
Family: DUF3412 (1)
(-)
Vibrio cholerae (1)
2aDUF3412-2pmbD05D:334-456
2bDUF3412-2pmbD06D:334-456
2cDUF3412-2pmbD07D:334-456
2dDUF3412-2pmbD08D:334-456

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9KTK3_VIBCH | Q9KTK3)
molecular function
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0009691    cytokinin biosynthetic process    The chemical reactions and pathways resulting in the formation of cytokinins, a class of adenine-derived compounds that can function in plants as growth regulators.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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
(no "Cis Peptide Bonds" information available for 2pmb)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2pmb
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9KTK3_VIBCH | Q9KTK3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9KTK3_VIBCH | Q9KTK3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9KTK3_VIBCH | Q9KTK3: 3gh1 4npa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PMB)