Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF OMPA-LIKE DOMAIN FROM ACINETOBACTER BAUMANNII IN COMPLEX WITH GLYCINE
 
Authors :  J. S. Park, W. C. Lee, J. H. Song, H. Y. Kim
Date :  10 Aug 11  (Deposition) - 26 Oct 11  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  E,H  (1x)
Biol. Unit 4:  F,G  (1x)
Keywords :  Ompa-Like Fold, Cell-Wall Attachment, Peptidoglycan-Binding, Membrane Protein, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. S. Park, W. C. Lee, K. J. Yeo, K. S. Ryu, M. Kumarasiri, D. Hesek, M. Lee S. Mobashery, J. H. Song, S. I. Kim, J. C. Lee, C. Cheong, Y. H. Jeon, H. Y. Kim
Mechanism Of Anchoring Of Ompa Protein To The Cell Wall Peptidoglycan Of The Gram-Negative Bacterial Outer Membrane
Faseb J. V. 26 219 2012
PubMed-ID: 21965596  |  Reference-DOI: 10.1096/FJ.11-188425

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN OMP38
    ChainsA, B, C, D, E, F, G, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentC-TERMINAL DOMAIN
    GeneOMP38
    Organism ScientificACINETOBACTER BAUMANNII
    Organism Taxid470
    SynonymABOMPA, OUTER MEMBRANE PROTEIN OMPA, OUTER MEMBRANE PROTEIN OMPAB

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)A C     
Biological Unit 2 (1x) B D    
Biological Unit 3 (1x)    E  H
Biological Unit 4 (1x)     FG 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1GLY8Mod. Amino AcidGLYCINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:236 , ASN A:237 , THR A:270 , ASP A:271 , THR A:273 , ASN A:279 , LEU A:282 , ARG A:286 , ARG A:329BINDING SITE FOR RESIDUE GLY A 101
2AC2SOFTWARETHR B:236 , ASN B:237 , THR B:270 , ASP B:271 , THR B:273 , ASN B:279 , LEU B:282 , ARG B:286 , ARG B:329BINDING SITE FOR RESIDUE GLY B 201
3AC3SOFTWARETHR C:236 , ASN C:237 , THR C:270 , ASP C:271 , THR C:273 , ASN C:279 , LEU C:282 , ARG C:286 , ARG C:329BINDING SITE FOR RESIDUE GLY C 340
4AC4SOFTWARETHR D:236 , ASN D:237 , THR D:270 , ASP D:271 , THR D:273 , ASN D:279 , LEU D:282 , ARG D:286 , ARG D:329BINDING SITE FOR RESIDUE GLY D 401
5AC5SOFTWARETHR E:236 , ASN E:237 , THR E:270 , ASP E:271 , THR E:273 , ASN E:279 , LEU E:282 , ARG E:286 , ARG E:329BINDING SITE FOR RESIDUE GLY E 501
6AC6SOFTWARETHR F:236 , ASN F:237 , THR F:270 , ASP F:271 , THR F:273 , ASN F:279 , LEU F:282 , ARG F:286 , ARG F:329BINDING SITE FOR RESIDUE GLY F 601
7AC7SOFTWARETHR G:236 , ASN G:237 , THR G:270 , ASP G:271 , THR G:273 , ASN G:279 , LEU G:282 , ARG G:286 , ARG G:329BINDING SITE FOR RESIDUE GLY G 701
8AC8SOFTWARETHR H:236 , ASN H:237 , THR H:270 , ASP H:271 , THR H:273 , ASN H:279 , LEU H:282 , ARG H:286 , ARG H:329BINDING SITE FOR RESIDUE GLY H 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TD3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TD3)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPA_2PS51123 OmpA-like domain profile.OMP38_ACIBA221-339
 
 
 
 
 
 
 
  8A:221-339
B:221-339
C:221-339
D:221-339
E:221-339
F:221-339
G:221-339
H:221-339
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPA_2PS51123 OmpA-like domain profile.OMP38_ACIBA221-339
 
 
 
 
 
 
 
  2A:221-339
-
C:221-339
-
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPA_2PS51123 OmpA-like domain profile.OMP38_ACIBA221-339
 
 
 
 
 
 
 
  2-
B:221-339
-
D:221-339
-
-
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPA_2PS51123 OmpA-like domain profile.OMP38_ACIBA221-339
 
 
 
 
 
 
 
  2-
-
-
-
E:221-339
-
-
H:221-339
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPA_2PS51123 OmpA-like domain profile.OMP38_ACIBA221-339
 
 
 
 
 
 
 
  2-
-
-
-
-
F:221-339
G:221-339
-

(-) Exons   (0, 0)

(no "Exon" information available for 3TD3)

(-) 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:121
 aligned with OMP38_ACIBA | Q6RYW5 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:127
                                   229       239       249       259       269       279       289       299       309       319       329       339       
          OMP38_ACIBA   220 QELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRTVVVQPG 346
               SCOP domains d3td3a_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeeeeeeee------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -OMPA_2  PDB: A:221-339 UniProt: 221-339                                                                                ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td3 A 220 MELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR------G 101
                                   229       239       249       259       269       279       289       299       309       319       329       339      |
                                                                                                                                                 339    101

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with OMP38_ACIBA | Q6RYW5 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:127
                                   229       239       249       259       269       279       289       299       309       319       329       339       
          OMP38_ACIBA   220 QELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRTVVVQPG 346
               SCOP domains d3td3b_ B: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee...........hhhhhhhhheeeeeeeee.------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -OMPA_2  PDB: B:221-339 UniProt: 221-339                                                                                ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td3 B 220 MELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR------G 201
                                   229       239       249       259       269       279       289       299       309       319       329       339      |
                                                                                                                                                 339    201

Chain C from PDB  Type:PROTEIN  Length:121
 aligned with OMP38_ACIBA | Q6RYW5 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:127
                                   229       239       249       259       269       279       289       299       309       319       329       339       
          OMP38_ACIBA   220 QELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRTVVVQPG 346
               SCOP domains d3td3c_ C: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeeeeeeee------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -OMPA_2  PDB: C:221-339 UniProt: 221-339                                                                                ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td3 C 220 MELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR------G 340
                                   229       239       249       259       269       279       289       299       309       319       329       339      |
                                                                                                                                                 339    340

Chain D from PDB  Type:PROTEIN  Length:123
 aligned with OMP38_ACIBA | Q6RYW5 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:129
                                   227       237       247       257       267       277       287       297       307       317       327       337         
          OMP38_ACIBA   218 QPQELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRTVVVQPG 346
               SCOP domains d3td3d_ D: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee...........hhhhhhhhheeeeeeeee.------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---OMPA_2  PDB: D:221-339 UniProt: 221-339                                                                                ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td3 D 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR------G 401
                                   227       237       247       257       267       277       287       297       307       317       327       337 |      |
                                                                                                                                                   339    401

Chain E from PDB  Type:PROTEIN  Length:121
 aligned with OMP38_ACIBA | Q6RYW5 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:127
                                   229       239       249       259       269       279       289       299       309       319       329       339       
          OMP38_ACIBA   220 QELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRTVVVQPG 346
               SCOP domains d3td3e_ E: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee...........hhhhhhhhheeeeeeeeee------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -OMPA_2  PDB: E:221-339 UniProt: 221-339                                                                                ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td3 E 220 MELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR------G 501
                                   229       239       249       259       269       279       289       299       309       319       329       339      |
                                                                                                                                                 339    501

Chain F from PDB  Type:PROTEIN  Length:123
 aligned with OMP38_ACIBA | Q6RYW5 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:129
                                   227       237       247       257       267       277       287       297       307       317       327       337         
          OMP38_ACIBA   218 QPQELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRTVVVQPG 346
               SCOP domains d3td3f_ F: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee...........hhhhhhhhheeeeeeeee.------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---OMPA_2  PDB: F:221-339 UniProt: 221-339                                                                                ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td3 F 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR------G 601
                                   227       237       247       257       267       277       287       297       307       317       327       337 |      |
                                                                                                                                                   339    601

Chain G from PDB  Type:PROTEIN  Length:123
 aligned with OMP38_ACIBA | Q6RYW5 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:129
                                   227       237       247       257       267       277       287       297       307       317       327       337         
          OMP38_ACIBA   218 QPQELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRTVVVQPG 346
               SCOP domains d3td3g_ G: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee...........hhhhhhhhheeeeeeeee.------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---OMPA_2  PDB: G:221-339 UniProt: 221-339                                                                                ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td3 G 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR------G 701
                                   227       237       247       257       267       277       287       297       307       317       327       337 |      |
                                                                                                                                                   339    701

Chain H from PDB  Type:PROTEIN  Length:122
 aligned with OMP38_ACIBA | Q6RYW5 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:128
                                   228       238       248       258       268       278       288       298       308       318       328       338        
          OMP38_ACIBA   219 PQELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRTVVVQPG 346
               SCOP domains d3td3h_ H: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee...........hhhhhhhhheeeeeeeeee------. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --OMPA_2  PDB: H:221-339 UniProt: 221-339                                                                                ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3td3 H 219 HMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR------G 801
                                   228       238       248       258       268       278       288       298       308       318       328       338|      |
                                                                                                                                                  339    801

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (1, 8)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TD3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TD3)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (OMP38_ACIBA | Q6RYW5)
molecular function
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
biological process
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GLY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3td3)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3td3
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  OMP38_ACIBA | Q6RYW5
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  OMP38_ACIBA | Q6RYW5
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        OMP38_ACIBA | Q6RYW53td4 3td5 4g4y 4g4z 4g88

(-) Related Entries Specified in the PDB File

3td4 3td5