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(-) Description

Title :  STRUCTURE OF THE PBP NOCT-M117N IN COMPLEX WITH PYRONOPALINE
 
Authors :  S. Morera, A. Vigouroux
Date :  26 Feb 14  (Deposition) - 22 Oct 14  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
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
    Mutation: YES
    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  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2OP12Ligand/Ion1-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-5-OXO-D-PROLINE
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2OP11Ligand/Ion1-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-5-OXO-D-PROLINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2OP11Ligand/Ion1-[(1S)-4-CARBAMIMIDAMIDO-1-CARBOXYBUTYL]-5-OXO-D-PROLINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:36 , TYR A:39 , TRP A:77 , ALA A:94 , ALA A:95 , GLY A:97 , ARG A:102 , ASN A:117 , GLN A:165 , THR A:168 , SER A:169 , HIS A:170 , SER A:207 , SER A:209 , PHE A:235 , HOH A:405BINDING SITE FOR RESIDUE OP1 A 301
02AC2SOFTWAREPRO A:41 , LYS A:217 , TRP A:274 , HOH A:408 , HOH A:642 , HOH A:684 , HOH B:555BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWARETHR A:32 , ARG A:88 , TYR A:89 , HOH A:593BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREPRO A:144 , HOH A:459 , HOH A:704BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREGLN A:272 , TYR A:277 , ASP A:278 , HOH A:685 , HOH A:708BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREGLN A:75 , ALA A:76 , GLY A:79 , LYS A:155BINDING SITE FOR RESIDUE PEG A 306
07AC7SOFTWARELYS A:104 , LYS A:175 , EDO A:310 , HOH A:481 , HOH A:681BINDING SITE FOR RESIDUE PEG A 307
08AC8SOFTWAREGLU A:103 , PRO A:179 , SER A:180 , GLN A:182 , HOH A:443 , HOH A:625BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREARG A:65 , ASN A:67 , GLN B:176BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWARELYS A:104 , LYS A:175 , ILE A:183 , THR A:185 , PEG A:307 , HOH A:421 , HOH A:501BINDING SITE FOR RESIDUE EDO A 310
11BC2SOFTWAREGLU B:36 , TYR B:39 , TRP B:77 , ALA B:94 , ALA B:95 , GLY B:97 , ARG B:102 , ASN B:117 , GLN B:165 , THR B:168 , SER B:169 , HIS B:170 , SER B:207 , HOH B:401BINDING SITE FOR RESIDUE OP1 B 301
12BC3SOFTWARELEU B:139 , ASP B:140 , MET B:177 , GLY B:233 , LEU B:234BINDING SITE FOR RESIDUE PEG B 302
13BC4SOFTWAREALA B:133 , ILE B:134 , GLU B:135 , ASN B:136 , HOH B:563BINDING SITE FOR RESIDUE EDO B 303
14BC5SOFTWARELYS B:212 , ARG B:229 , HOH B:568BINDING SITE FOR RESIDUE EDO B 304
15BC6SOFTWAREALA B:40 , PRO B:41 , PRO B:213 , LEU B:214 , LYS B:217 , HOH B:413 , HOH B:427 , HOH B:461BINDING SITE FOR RESIDUE EDO B 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PP0)

(-) 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 4PP0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PP0)

(-) Exons   (0, 0)

(no "Exon" information available for 4PP0)

(-) 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....hhhhhhhhhhhhhhh....eeee..hhhhhhhhhhh....eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeeeeeeeehhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pp0 A  28 YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPNTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASP 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: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
                 4pp0 B  28 YKSITIATEGSYAPYNFKDAGGKLIGFDIDLGNDLCKRMNIECKFVEQAWDGIIPSLTAGRYDAIMAAMGIQPAREKVIAFSRPYLLTPNTFLTTADSPLLKTQVAIENLPLDNITPEQKAELDKFTKIFEGVKFGVQAGTSHEAFMKQMMPSVQISTYDTIDNVVMDLKAGRIDASLASVSFLKPLTDKPDNKDLKMFGPRMTGGLFGKGVGVGIRKEDADLKALFDKAIDAAIADGTVQKLSQQWFGYDASPK 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)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4PP0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PP0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PP0)

(-) 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 4pox 5ito 5itp

(-) Related Entries Specified in the PDB File

4p0i 4pow 4pox