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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI OMPF PORIN IN COMPLEX WITH CARBENICILLIN
 
Authors :  B. K. Ziervogel, B. Roux
Date :  30 Jul 12  (Deposition) - 19 Dec 12  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Beta-Barrel, Protein-Drug Complex, Trimer, Non-Specific Channel, Carbenicillin Binding, Outer Membrane, Membrane Protein-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Ziervogel, B. Roux
The Binding Of Antibiotics In Ompf Porin.
Structure V. 21 76 2013
PubMed-ID: 23201272  |  Reference-DOI: 10.1016/J.STR.2012.10.014

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN F
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 23-362
    Gene: OMPF, CMLB, COA, CRY, TOLF, B0929, JW0912
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: OUTER MEMBRANE PROTEIN 1A, OUTER MEMBRANE PROTEIN B, OUTER MEMBRANE PROTEIN IA, PORIN OMPF

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
10JM2Ligand/Ion(2S,5R,6R,7R)-6-{[(2R)-2-CARBOXY-2-PHENYLACETYL]AMINO}-7-HYDROXY-3,3-DIMETHYL-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
10JM3Ligand/Ion(2S,5R,6R,7R)-6-{[(2R)-2-CARBOXY-2-PHENYLACETYL]AMINO}-7-HYDROXY-3,3-DIMETHYL-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
10JM3Ligand/Ion(2S,5R,6R,7R)-6-{[(2R)-2-CARBOXY-2-PHENYLACETYL]AMINO}-7-HYDROXY-3,3-DIMETHYL-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:15 , LYS A:16 , ARG A:42 , LYS A:46 , GLN A:60 , GLU A:62 , ARG A:82BINDING SITE FOR RESIDUE 0JM A 401
2AC2SOFTWARETYR B:14 , GLY B:15 , LYS B:16 , ARG B:42 , LYS B:46 , GLU B:62 , ARG B:82 , GLN B:339BINDING SITE FOR RESIDUE 0JM B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:27 -Gly A:28
2Asn B:27 -Gly B:28

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GCQ)

(-) 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:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gcqa_ A: Porin                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee............ee..eeeeeeeeeeeee..eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeeehhhhhh....eeeeeee......hhhhh...eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eee......eee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeee....eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gcq A   8 GNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    17        27        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       287       297       307       317       327       337   


Chain B from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gcqb_ B: Porin                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee............ee..eeeeeeeeeeeee..eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeee..hhhhhh.....................eeeeeeeeeehhhhhh...eeeeeeee..............eeeeeeeeee..eeeeeeeeeee.hhhhhh.......eeeeeeeeeeeee..eeeeeeeeeee...eee......eee..eeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee..eeeeeeeeee..............eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gcq B   8 GNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF 340
                                    17        27        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       287       297       307       317       327       337
   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  (1, 2)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        OMPF_ECOLI | P02931: 1bt9 1gfm 1gfn 1gfo 1gfp 1gfq 1hxt 1hxu 1hxx 1mpf 1opf 2omf 2zfg 2zld 3fyx 3hw9 3hwb 3k19 3k1b 3o0e 3poq 3pou 3pox 4d5u 4gcp 4gcs 4jfb 4lse 4lsf 4lsh 4lsi

(-) Related Entries Specified in the PDB File

4gcp E. COLI OMPF IN COMPLEX WITH AMPICILLIN
4gcs E. COLI OMPF IN COMPLEX WITH ERTAPENEM