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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA OCCK2 (OPDF) IN COMPLEX WITH GLUCURONATE
 
Authors :  B. Van Den Berg, E. Eren
Date :  18 Jun 12  (Deposition) - 13 Mar 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Beta-Barrel, Outer Membrane Transporter (Porin), Glucuronate, Outer Membrane, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Eren, J. Parkin, A. Adelanwa, B. Cheneke, L. Movileanu, S. Khalid, B. Van Den Berg
Toward Understanding The Outer Membrane Uptake Of Small Molecules By Pseudomonas Aeruginosa.
J. Biol. Chem. V. 288 12042 2013
PubMed-ID: 23467408  |  Reference-DOI: 10.1074/JBC.M113.463570

(-) Compounds

Molecule 1 - PROBABLE PORIN
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 25-421
    Gene: PA0240
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1BDP2Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
2C8E7Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3PGV4Ligand/Ion(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1BDP1Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
2C8E4Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3PGV1Ligand/Ion(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
1BDP1Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
2C8E3Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3PGV3Ligand/Ion(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
4SO42Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:126 , ARG B:129 , ARG B:161 , ARG B:280 , SER B:285 , GLY B:286 , ASP B:292 , TYR B:294 , ASN B:295 , ALA B:296 , SER B:297 , HOH B:516 , HOH B:536BINDING SITE FOR RESIDUE BDP B 401
02AC2SOFTWAREARG B:161 , ASN B:162 , HOH B:561 , HOH B:595BINDING SITE FOR RESIDUE SO4 B 402
03AC3SOFTWAREARG B:97 , MET B:166BINDING SITE FOR RESIDUE SO4 B 403
04AC4SOFTWAREPHE A:314 , LEU A:317 , PHE A:324 , C8E A:404 , PHE B:324 , THR B:326 , SER B:350 , TRP B:368BINDING SITE FOR RESIDUE C8E B 404
05AC5SOFTWARETYR A:354 , HIS B:25 , ASN B:27 , ASN B:370 , ASN B:386 , C8E B:407BINDING SITE FOR RESIDUE C8E B 405
06AC6SOFTWAREGLN B:270 , SER B:305BINDING SITE FOR RESIDUE C8E B 406
07AC7SOFTWARELEU A:352 , TYR B:310 , PHE B:312 , C8E B:405BINDING SITE FOR RESIDUE C8E B 407
08AC8SOFTWARELEU B:17 , PHE B:44 , LEU B:46 , LEU B:66 , TYR B:67 , GLY B:96 , ARG B:97 , ARG B:235 , ARG B:250 , VAL B:252BINDING SITE FOR RESIDUE PGV B 408
09AC9SOFTWAREASP A:126 , ARG A:129 , ARG A:161 , ARG A:280 , SER A:285 , GLY A:286 , ASP A:292 , TYR A:294 , ASN A:295 , ALA A:296 , SER A:297 , HOH A:521 , HOH A:547BINDING SITE FOR RESIDUE BDP A 401
10BC1SOFTWAREHIS A:2 , VAL A:3 , HIS A:4 , GLN A:54 , GLY A:55 , HOH A:536BINDING SITE FOR RESIDUE SO4 A 402
11BC2SOFTWAREARG A:161 , ASN A:162 , HOH A:546 , HOH A:615 , HOH A:616BINDING SITE FOR RESIDUE SO4 A 403
12BC3SOFTWAREHIS A:263 , TYR A:310 , TYR B:328 , C8E B:404BINDING SITE FOR RESIDUE C8E A 404
13BC4SOFTWAREPHE A:256 , ALA A:258 , LEU A:267 , PHE A:361BINDING SITE FOR RESIDUE C8E A 405
14BC5SOFTWAREALA A:19 , PHE A:44 , ALA A:254 , PHE A:256 , LEU A:269 , GLN A:270BINDING SITE FOR RESIDUE C8E A 406
15BC6SOFTWARESER A:56BINDING SITE FOR RESIDUE PGV A 407
16BC7SOFTWAREPHE A:9 , LEU A:10 , GLU A:11 , THR A:53 , GLN A:54 , HOH A:579 , HOH A:614BINDING SITE FOR RESIDUE PGV A 408
17BC8SOFTWARELEU A:66 , TYR A:67 , GLY A:96 , ARG A:97 , ARG A:235 , ARG A:250BINDING SITE FOR RESIDUE PGV A 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FMS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FMS)

(-) 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:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeeeeeeee..eeeeeeeeeeeeee.......eeeeeeeeeeeeee....eeeeeeeeeeeee..eeeeeeee..ee..ee.........eeeeeeeee.....eeeeeeeeeeee.........eee..eeeeee..eeeeeeeeee....eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee..............................eeeeeeeeee.hhhh...eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee.........eeeeeeeeeee...eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fms A   1 GHVHAGQGFLEDAKASLTARNFHLHRNFVGKAEEWTQSFILDARSGFTQGSVGFGLDVLGLYSLKLDADDFGRLAVAGKLRVSNSELKIGEWMPVLPILRSDDGRSLPQTFRGGQLSANEIAGLTLYAGQFRGNSPRNDASMQDMSLFGRPAATSDRFDFAGGEYRFNGERSLLGLWNAELKDIYRQQYLQLQHSQPLGDWLLGANLGGFRGRDAGSARAGKLDNRTVSALFSARYGLHTLYLGLQKVSGDDGWMRVNGTSGGTLANDSYNASYDNPGERSWQLRYDFDFVGLGLPGLTFMTRYLHGDHVRLAGVTDDGSEWGRESELGYTLQSGAFKRLNVRWRNSSQRRDWRFDENRLIVSYPLSLL 397
                                    10        20        35        45        55        65      ||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  ||   388         
                                                       29|                                   72|                                                                                                                                                                                                                                                                                          377|               
                                                        35                                    92                                                                                                                                                                                                                                                                                           382               


Chain B from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeeee...eeeeeeeeeeeeee.......eeeeeeeeeeeeee....eeeeeeeeeeeee..eeeeeeee..ee..ee.........eeeeeeeee.....eeeeeeeeeeee.........eee..eeeeee..eeeeeeeeee....eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee..............................eeeeeeeeee.hhhh...eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee.........eeeeeeeeeee.......eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fms B   7 QGFLEDAKASLTARNFHLHRNFVGGKAEEWTQSFILDARSGFTQGSVGFGLDVLGLYSLKLDADDFGRLAVAGKLRVSNSELKIGEWMPVLPILRSDDGRSLPQTFRGGQLSANEIAGLTLYAGQFRGNSPRNDASMQDMSLFGRPAATSDRFDFAGGEYRFNGERSLLGLWNAELKDIYRQQYLQLQHSQPLGDWLLGANLGGFRGRDAGSARAGKLDNRTVSALFSARYGLHTLYLGLQKVSGDDGWMRVNGTSGGTLANDSYNASYDNPGERSWQLRYDFDFVGLGLPGLTFMTRYLHGDHVRLAGVTDDGSEWGRESELGYTLQSGAFKRLNVRWRNSSQRRDWGSNTRFDENRLIVSYPLSLL 397
                                    16        26   ||   40        50        60        70 ||     99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
                                                  30|                                   72|                                                                                                                                                                                                                                                                                                                 
                                                   35                                    92
   Legend:   → Mismatch (orange background)
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    → 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 4FMS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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        Q9I6P8_PSEAE | Q9I6P8: 3szd

(-) Related Entries Specified in the PDB File

3szd CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA OCCK2 (OPDF)