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 PEPTIDOGLYCAN-BINDING DOMAIN FROM ACINETOBACTER BAUMANNII
 
Authors :  W. C. Lee, J. H. Song, J. S. Park, H. Y. Kim
Date :  22 Jul 12  (Deposition) - 24 Jul 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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 Domain, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Lee, J. S. Park, J. H. Song, S. I. Kim, J. C. Lee, J. Cheong, H. Y. Kim
Enantiomer-Dependent Amino Acid Binding Affinity Of Ompa-Like Domains From Acinetobacter Baumannii Peptidoglycan-Associated Lipoprotein And Ompa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN OMP38
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PEPTIDOGLYCAN-BINDING DOMAIN, UNP RESIDUES 221-339
    Gene: OMP38, OMPA
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470
    Synonym: 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  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1API8Ligand/Ion2,6-DIAMINOPIMELIC ACID
2SRT2Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1API2Ligand/Ion2,6-DIAMINOPIMELIC ACID
2SRT-1Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1API2Ligand/Ion2,6-DIAMINOPIMELIC ACID
2SRT1Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1API2Ligand/Ion2,6-DIAMINOPIMELIC ACID
2SRT-1Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1API2Ligand/Ion2,6-DIAMINOPIMELIC ACID
2SRT1Ligand/IonS,R MESO-TARTARIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:236 , ASN A:237 , THR A:270 , ASP A:271 , THR A:273 , GLY A:274 , ASN A:279 , LEU A:282 , ARG A:286 , ARG A:329 , HOH A:549 , HOH A:573 , HOH E:530BINDING SITE FOR RESIDUE API A 401
02AC2SOFTWARETHR B:236 , ASN B:237 , THR B:270 , ASP B:271 , THR B:273 , GLY B:274 , PRO B:275 , ASN B:279 , LEU B:282 , ARG B:286 , ARG B:329BINDING SITE FOR RESIDUE API B 401
03AC3SOFTWARETHR 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 API C 401
04AC4SOFTWARETHR D:236 , ASN D:237 , THR D:270 , ASP D:271 , THR D:273 , GLY D:274 , PRO D:275 , ASN D:279 , LEU D:282 , ARG D:286 , ARG D:329 , HOH D:535BINDING SITE FOR RESIDUE API D 401
05AC5SOFTWAREGLY D:217 , SER D:218 , THR D:236 , LYS D:322 , ARG D:325 , ALA D:326 , ARG D:329 , HOH D:512 , HOH D:524BINDING SITE FOR RESIDUE SRT D 402
06AC6SOFTWARETHR E:236 , ASN E:237 , THR E:270 , ASP E:271 , THR E:273 , GLY E:274 , ASN E:279 , LEU E:282 , ARG E:286 , ARG E:329 , HOH E:558BINDING SITE FOR RESIDUE API E 401
07AC7SOFTWARETHR F:236 , ASN F:237 , THR F:270 , ASP F:271 , THR F:273 , GLY F:274 , PRO F:275 , ASN F:279 , LEU F:282 , ARG F:286 , ARG F:329 , HOH F:543 , HOH F:606BINDING SITE FOR RESIDUE API F 401
08AC8SOFTWARETHR G:236 , ASN G:237 , THR G:270 , ASP G:271 , THR G:273 , GLY G:274 , PRO G:275 , ASN G:279 , LEU G:282 , ARG G:286 , ARG G:329 , HOH G:545 , HOH G:578 , HOH G:587BINDING SITE FOR RESIDUE API G 401
09AC9SOFTWAREGLY G:217 , SER G:218 , THR G:236 , LYS G:322 , ARG G:325 , ALA G:326 , ARG G:329 , HOH G:516 , HOH G:519 , HOH G:539 , HOH G:592 , HOH G:612 , HOH G:615BINDING SITE FOR RESIDUE SRT G 402
10BC1SOFTWARETHR H:236 , ASN H:237 , THR H:270 , ASP H:271 , THR H:273 , GLY H:274 , PRO H:275 , ASN H:279 , LEU H:282 , ARG H:286 , ARG H:329 , HOH H:541BINDING SITE FOR RESIDUE API H 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G88)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G88)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G88)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G88)

(-) Exons   (0, 0)

(no "Exon" information available for 4G88)

(-) 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:122
                                                                                                                                                          
               SCOP domains d4g88a_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g88 A 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR 339
                                   227       237       247       257       267       277       287       297       307       317       327       337  


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4g88b_ B: 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 -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g88 B 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR 339
                                   227       237       247       257       267       277       287       297       307       317       327       337  


Chain C from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4g88c_ C: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee...........hhhhhhhhheeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g88 C 220 MELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR 339
                                   229       239       249       259       269       279       289       299       309       319       329       339


Chain D from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4g88d_ D: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g88 D 217 GSHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR 339
                                   226       236       246       256       266       276       286       296       306       316       326       336   


Chain E from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4g88e_ E: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee...........hhhhhhhhheeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g88 E 220 MELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR 339
                                   229       239       249       259       269       279       289       299       309       319       329       339


Chain F from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4g88f_ 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 -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g88 F 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR 339
                                   227       237       247       257       267       277       287       297       307       317       327       337  


Chain G from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4g88g_ G: 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 --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g88 G 217 GSHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR 339
                                   226       236       246       256       266       276       286       296       306       316       326       336   


Chain H from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d4g88h_ 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 ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g88 H 219 HMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSR 339
                                   228       238       248       258       268       278       288       298       308       318       328       338
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G88)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G88)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

 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
    API  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SRT  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4g88)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4g88
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  OMP38_ACIBA | Q6RYW5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  OMP38_ACIBA | Q6RYW5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        OMP38_ACIBA | Q6RYW5: 3td3 3td4 3td5 4g4y 4g4z

(-) Related Entries Specified in the PDB File

4g4v 4g4w 4g4x 4g4y 4g4z