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
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)

(-) Description

Title :  COMPLEX OF VANCOMYCIN WITH N-ACETYL GLYCINE
 
Authors :  P. J. Loll, J. Kaplan, B. Selinsky, P. H. Axelsen
Date :  15 Jul 99  (Deposition) - 16 Aug 99  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Glycopeptide, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Loll, J. Kaplan, B. S. Selinsky, P. H. Axelsen
Vancomycin Binding To Low-Affinity Ligands: Delineating A Minimum Set Of Interactions Necessary For High-Affinity Binding.
J. Med. Chem. V. 42 4714 1999
PubMed-ID: 10579833  |  Reference-DOI: 10.1021/JM990361T

(-) Compounds

Molecule 1 - VANCOMYCIN
    Chains: A, B
    Engineered: YES
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 20)

Asymmetric Unit (9, 20)
No.NameCountTypeFull Name
13FG2Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2AAC1Ligand/IonACETYLAMINO-ACETIC ACID
3BGC2Ligand/IonBETA-D-GLUCOSE
4CL3Ligand/IonCHLORIDE ION
5GHP4Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6MLU2Mod. Amino AcidN-METHYLLEUCINE
7OMY2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RER2Ligand/Ion(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
Biological Unit 1 (7, 8)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2AAC-1Ligand/IonACETYLAMINO-ACETIC ACID
3BGC1Ligand/IonBETA-D-GLUCOSE
4CL-1Ligand/IonCHLORIDE ION
5GHP2Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6MLU1Mod. Amino AcidN-METHYLLEUCINE
7OMY1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RER1Ligand/Ion(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
Biological Unit 2 (7, 16)
No.NameCountTypeFull Name
13FG2Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2AAC-1Ligand/IonACETYLAMINO-ACETIC ACID
3BGC2Ligand/IonBETA-D-GLUCOSE
4CL-1Ligand/IonCHLORIDE ION
5GHP4Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6MLU2Mod. Amino AcidN-METHYLLEUCINE
7OMY2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RER2Ligand/Ion(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:120 , HOH A:139 , HOH A:143 , MLU B:1 , OMZ B:2 , ASN B:3 , GHP B:4 , BGC B:8 , CL B:12BINDING SITE FOR RESIDUE AAC B 11
2AC2SOFTWAREOMZ A:2 , RER A:9 , MLU B:1 , RER B:9BINDING SITE FOR RESIDUE CL A 12
3AC3SOFTWAREASN A:3 , 3FG A:7 , OMZ B:2BINDING SITE FOR RESIDUE CL A 13
4AC4SOFTWAREOMY B:6 , 3FG B:7 , AAC B:11BINDING SITE FOR RESIDUE CL B 12
5AC5SOFTWARECL A:12 , CL A:13 , HOH A:110 , HOH A:111 , HOH A:112 , HOH A:116 , HOH A:118 , HOH A:122 , HOH A:126 , HOH A:129 , HOH A:134 , HOH A:138 , HOH A:140 , HOH A:141 , HOH A:142 , HOH A:144 , HOH A:145 , HOH A:147 , HOH A:149 , MLU B:1 , OMZ B:2 , ASN B:3 , GHP B:4 , GHP B:5 , OMY B:6 , 3FG B:7 , BGC B:8 , RER B:9BINDING SITE FOR CHAIN A OF VANCOMYCIN
6AC6SOFTWAREMLU A:1 , OMZ A:2 , ASN A:3 , GHP A:4 , GHP A:5 , OMY A:6 , 3FG A:7 , BGC A:8 , RER A:9 , CL A:12 , CL A:13 , HOH A:111 , HOH A:119 , HOH A:123 , HOH A:124 , HOH A:125 , HOH A:127 , HOH A:130 , HOH A:131 , HOH A:133 , HOH A:136 , HOH A:140 , HOH A:142 , HOH A:147 , HOH A:148 , AAC B:11 , CL B:12BINDING SITE FOR CHAIN B OF VANCOMYCIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QD8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ghp A:5 -Omy A:6
2Ghp B:5 -Omy B:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QD8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QD8)

(-) Exons   (0, 0)

(no "Exon" information available for 1QD8)

(-) 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:7
                                     
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                   1qd8 A 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG


Chain B from PDB  Type:PROTEIN  Length:7
                                     
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                   1qd8 B 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG
   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  (0, 0)

(no "SCOP Domain" information available for 1QD8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1QD8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QD8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1QD8)

 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
    3FG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AAC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GHP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OMY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OMZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RER  [ 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 ]
 
  Cis Peptide Bonds
    Ghp A:5 - Omy A:6   [ RasMol ]  
    Ghp B:5 - Omy B:6   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  1qd8
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1QD8)

(-) Related Entries Specified in the PDB File

1aa5 CRYSTAL STRUCTURE OF VANCOMYCIN
1c0q CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH 2-ACETOXY-D- PROPANOIC ACID
1c0r CRYSTAL STRUCTURE OF VANCOMYCIN WITH D-LACTIC ACID
1fvm CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH DI-ACETYL- LYS-D-ALA-D-ALA
1gac SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT
1ghg CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON
1pn3 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXD WITH TDP AND DESVANCOSAMINYL VANCOMYCIN
1pnv CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXED WITH TDP AND VANCOMYCIN
1rrv CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEXED WITH TDP AND DESVANCOSAMINYL VANCOMYCIN.
1sho CRYSTAL STRUCTURE OF VANCOMYCIN