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(-) 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 :  16 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, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1ALA8Mod. Amino AcidALANINE
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ALA2Mod. Amino AcidALANINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ALA2Mod. Amino AcidALANINE
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1ALA2Mod. Amino AcidALANINE
2SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1ALA2Mod. Amino AcidALANINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR 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 ALA A 401
02AC2SOFTWARETHR A:236 , LYS A:322 , ARG A:325 , ARG A:329 , HOH A:514 , HOH A:523BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWARETHR 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 ALA B 401
04AC4SOFTWARETHR B:236 , LYS B:322 , ARG B:325 , ARG B:329 , HOH B:566 , HOH B:569BINDING SITE FOR RESIDUE SO4 B 402
05AC5SOFTWARETHR 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 ALA C 401
06AC6SOFTWARETHR C:236 , ARG C:325 , ARG C:329 , HOH C:555BINDING SITE FOR RESIDUE SO4 C 402
07AC7SOFTWARETHR 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 ALA D 401
08AC8SOFTWARELYS D:322 , ARG D:325 , ARG D:329 , HOH D:512 , HOH D:564BINDING SITE FOR RESIDUE SO4 D 402
09AC9SOFTWARETHR 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 ALA E 401
10BC1SOFTWARETHR E:236 , LYS E:322 , ARG E:325 , ARG E:329 , HOH E:517 , HOH E:527 , HOH E:546BINDING SITE FOR RESIDUE SO4 E 402
11BC2SOFTWARETHR 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 ALA F 401
12BC3SOFTWARETHR F:236 , ARG F:325 , ARG F:329 , HOH F:554 , HOH F:563BINDING SITE FOR RESIDUE SO4 F 402
13BC4SOFTWARETHR 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 ALA G 401
14BC5SOFTWARETHR G:236 , LYS G:322 , ARG G:325 , ARG G:329 , HOH G:553 , HOH G:566BINDING SITE FOR RESIDUE SO4 G 402
15BC6SOFTWARETHR 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 ALA H 401
16BC7SOFTWARETHR H:236 , LYS H:322 , ARG H:325 , ARG H:329 , HOH H:532 , HOH H:534BINDING SITE FOR RESIDUE SO4 H 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G4Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G4Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4G4Y)

(-) 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
                                                                                                                                                         
               SCOP domains d4g4ya_ 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 ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g4y A 220 MELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRA 401
                                   229       239       249       259       269       279       289       299       309       319       329       339|
                                                                                                                                                 339|
                                                                                                                                                  401


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4g4yb_ 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
                 4g4y B 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRA 401
                                   227       237       247       257       267       277       287       297       307       317       327       337 ||
                                                                                                                                                   339|
                                                                                                                                                    401


Chain C from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d4g4yc_ 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
                 4g4y C 220 MELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRA 401
                                   229       239       249       259       269       279       289       299       309       319       329       339|
                                                                                                                                                 339|
                                                                                                                                                  401


Chain D from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4g4yd_ 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
                 4g4y D 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRA 401
                                   227       237       247       257       267       277       287       297       307       317       327       337 ||
                                                                                                                                                   339|
                                                                                                                                                    401


Chain E from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4g4ye_ 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
                 4g4y E 219 HMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRA 401
                                   228       238       248       258       268       278       288       298       308       318       328       338||
                                                                                                                                                  339|
                                                                                                                                                   401


Chain F from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4g4yf_ 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
                 4g4y F 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRA 401
                                   227       237       247       257       267       277       287       297       307       317       327       337 ||
                                                                                                                                                   339|
                                                                                                                                                    401


Chain G from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4g4yg_ G: 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
                 4g4y G 218 SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRA 401
                                   227       237       247       257       267       277       287       297       307       317       327       337 ||
                                                                                                                                                   339|
                                                                                                                                                    401


Chain H from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4g4yh_ 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
                 4g4y H 219 HMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIEGHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIADNKTKEGRAMNRRVFATITGSRA 401
                                   228       238       248       258       268       278       288       298       308       318       328       338||
                                                                                                                                                  339|
                                                                                                                                                   401
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  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 4G4Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G4Y)

(-) Gene Ontology  (8, 8)

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 Related Entries

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        OMP38_ACIBA | Q6RYW5: 3td3 3td4 3td5 4g4z 4g88

(-) Related Entries Specified in the PDB File

4g4v 4g4w 4g4x 4g4z 4g88