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(-) Description

Title :  STRUCTURE OF THE PBP NOCT IN COMPLEX WITH PYRONOPALINE
 
Authors :  S. Morera, A. Vigouroux
Date :  26 Feb 14  (Deposition) - 22 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pbp, Class F, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lang, A. Vigouroux, S. Planamente, A. El Sahili, P. Blin, M. Aumont-Nicaise, Y. Dessaux, S. Morera, D. Faure
Agrobacterium Uses A Unique Ligand-Binding Mode For Trappin Opines And Acquiring A Competitive Advantage In The Niche Construction On Plant Host.
Plos Pathog. V. 10 04444 2014
PubMed-ID: 25299655  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1004444

(-) Compounds

Molecule 1 - NOPALINE-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 26-283
    Gene: NOCT, ATU6027, AGR_PTI_67
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: C58 / ATCC 33970

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2OP12Ligand/Ion1-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-5-OXO-D-PROLINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2OP11Ligand/Ion1-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-5-OXO-D-PROLINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2OP11Ligand/Ion1-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-5-OXO-D-PROLINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:75 , LYS A:155BINDING SITE FOR RESIDUE EDO A 301
2AC2SOFTWAREGLY A:87 , ARG A:244BINDING SITE FOR RESIDUE EDO A 302
3AC3SOFTWAREGLU A:36 , TYR A:39 , TRP A:77 , ALA A:94 , ALA A:95 , GLY A:97 , ARG A:102 , MET A:117 , GLN A:165 , THR A:168 , SER A:169 , HIS A:170 , SER A:207 , HOH A:452BINDING SITE FOR RESIDUE OP1 A 303
4AC4SOFTWAREGLN A:272 , TYR A:277 , ASP A:278BINDING SITE FOR RESIDUE EDO A 304
5AC5SOFTWAREPRO A:138 , ASP A:140 , ASN A:141 , HOH A:473BINDING SITE FOR RESIDUE EDO A 305
6AC6SOFTWAREGLN A:273 , LYS B:221BINDING SITE FOR RESIDUE EDO A 306
7AC7SOFTWAREGLU B:36 , TYR B:39 , TRP B:77 , ALA B:94 , ALA B:95 , GLY B:97 , ARG B:102 , MET B:117 , GLN B:165 , THR B:168 , SER B:169 , HIS B:170 , SER B:207 , VAL B:239BINDING SITE FOR RESIDUE OP1 B 301
8AC8SOFTWAREGLN B:272 , ASP B:278 , HOH B:569BINDING SITE FOR RESIDUE EDO B 302

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:63 -A:70
2B:63 -B:70

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:40 -Pro A:41
2Ala B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4POW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4POW)

(-) Exons   (0, 0)

(no "Exon" information available for 4POW)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........ee.....eehhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh....ee......hhhhhh..ee........eeeeee..hhhhhh.....eee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pow A  28 YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASP 281
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277    


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........ee.....eehhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh....ee......hhhhhh..ee........eeeeee..hhhhhh.....eee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh.....eeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pow B  28 YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASP 281
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277
   Legend:   → Mismatch (orange background)
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  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 4POW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4POW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4POW)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  4pow
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 Related Entries

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

UniProtKB/Swiss-Prot
        NOCT_AGRFC | P35120: 4p0i 4pox 4pp0 5ito 5itp

(-) Related Entries Specified in the PDB File

4p0i 4pox 4pp0