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(-) Description

Title :  STRUCTURE OF THE PBP NOCT IN COMPLEX WITH NOPALINE
 
Authors :  S. Morera, A. Vigouroux
Date :  26 Feb 14  (Deposition) - 22 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
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  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
115P1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
22W22Ligand/IonN-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-D-GLUTAMICACID
3EDO7Ligand/Ion1,2-ETHANEDIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
115P1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
22W21Ligand/IonN-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-D-GLUTAMICACID
3EDO6Ligand/Ion1,2-ETHANEDIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
22W21Ligand/IonN-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-D-GLUTAMICACID
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:36 , TYR A:39 , ASN A:43 , TRP A:77 , ALA A:94 , ALA A:95 , GLY A:97 , ARG A:102 , THR A:115 , MET A:117 , GLN A:165 , THR A:168 , SER A:169 , HIS A:170 , SER A:207 , VAL A:239 , HOH A:418 , HOH A:419BINDING SITE FOR RESIDUE 2W2 A 301
02AC2SOFTWAREGLN A:99 , THR A:168 , GLU A:171 , ALA A:172 , GLN A:176 , EDO A:305BINDING SITE FOR RESIDUE 15P A 302
03AC3SOFTWARELYS A:104 , THR A:185BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREARG A:65 , ASP A:264BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWARETRP A:77 , ILE A:80 , ILE A:81 , ARG A:102 , GLY A:167 , 15P A:302 , HOH A:417BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREALA A:86BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWARELYS A:104 , GLU A:145 , SER A:184 , THR A:185BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREPRO A:126BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREARG A:200 , LYS A:245BINDING SITE FOR RESIDUE PEG A 309
10BC1SOFTWAREGLU 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 2W2 B 301
11BC2SOFTWARETHR B:168 , GLU B:171BINDING SITE FOR RESIDUE EDO B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4POX)

(-) 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 4POX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4POX)

(-) 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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee........ee.....eehhhhhhhhhhhhhhh.eeeeee....hhhhhhhh....ee........hhhhh.ee........eeeeee..hhhhhh.....eee....hhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pox A  27 DYKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASP 281
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276     


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........ee.....eehhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh....ee........hhhhh.ee........eeeeee..hhhhhh.....eee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh.....eeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pox B  28 YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPMTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASPK 282
                                    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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  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 4POX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        NOCT_AGRFC | P35120: 4p0i 4pow 4pp0 5ito 5itp

(-) Related Entries Specified in the PDB File

4p0i 4pow 4pp0