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 :  X-RAY CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD AS A COMPLEX WITH TDP AND THE NATURAL SUBSTRATE, DESVANCOSAMINYL VANCOMYCIN.
 
Authors :  A. M. Mulichak, W. Lu, H. C. Losey, C. T. Walsh, R. M. Garavito
Date :  09 Dec 03  (Deposition) - 18 May 04  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Gt-B, Glycosyltransferase, Rossmann Fold, Glycopeptide, Vacosamycin, Antibiotic, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Mulichak, W. Lu, H. C. Losey, C. T. Walsh, R. M. Garavito
Crystal Structure Of Vancosaminyltransferase Gtfd From The Vancomycin Biosynthetic Pathway: Interactions With Acceptor And Nucleotide Ligands
Biochemistry V. 43 5170 2004
PubMed-ID: 15122882  |  Reference-DOI: 10.1021/BI036130C

(-) Compounds

Molecule 1 - GLYCOSYLTRANSFERASE GTFD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GTFD
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958
 
Molecule 2 - DESVANCOSAMINYL VANCOMYCIN
    Chains: C, D
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 21)

Asymmetric Unit (9, 21)
No.NameCountTypeFull Name
13FG2Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC2Ligand/IonBETA-D-GLUCOSE
3GHP4Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
4GOL3Ligand/IonGLYCEROL
5K2Ligand/IonPOTASSIUM ION
6MLU2Mod. Amino AcidN-METHYLLEUCINE
7OMY2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ2Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9TYD2Ligand/IonTHYMIDINE-5'-DIPHOSPHATE
Biological Unit 1 (8, 10)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3GHP2Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
4GOL2Ligand/IonGLYCEROL
5K-1Ligand/IonPOTASSIUM ION
6MLU1Mod. Amino AcidN-METHYLLEUCINE
7OMY1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9TYD1Ligand/IonTHYMIDINE-5'-DIPHOSPHATE
Biological Unit 2 (8, 9)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3GHP2Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
4GOL1Ligand/IonGLYCEROL
5K-1Ligand/IonPOTASSIUM ION
6MLU1Mod. Amino AcidN-METHYLLEUCINE
7OMY1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9TYD1Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:311 , THR A:332 , ASP A:333 , GOL A:1006 , HOH A:2122 , HOH A:2266BINDING SITE FOR RESIDUE K A 417
2AC2SOFTWARETHR A:10 , ARG A:11 , GLY A:12 , ARG A:223 , GLY A:245 , SER A:246 , GLU A:293 , VAL A:294 , PHE A:296 , HIS A:309 , SER A:311 , GLY A:313 , THR A:314 , VAL A:317 , GOL A:1006 , HOH A:2010 , HOH A:2210 , HOH A:2298 , HOH A:2299 , HOH A:2300 , HOH A:2301BINDING SITE FOR RESIDUE TYD A 1003
3AC3SOFTWAREHIS A:58 , MET A:60 , GLN A:62 , MET A:65 , TRP A:276 , HOH A:2302 , HOH A:2303BINDING SITE FOR RESIDUE GOL A 1005
4AC4SOFTWAREGLY A:12 , ASP A:13 , PRO A:126 , SER A:311 , ALA A:312 , ASP A:333 , K A:417 , TYD A:1003 , BGC C:8 , HOH C:2013BINDING SITE FOR RESIDUE GOL A 1006
5AC5SOFTWARESER B:311 , THR B:332 , ASP B:333 , GOL B:1007 , HOH B:2044 , HOH B:2151BINDING SITE FOR RESIDUE K B 417
6AC6SOFTWARETHR B:10 , ARG B:11 , GLY B:12 , ARG B:223 , SER B:246 , GLU B:293 , VAL B:294 , PHE B:296 , HIS B:309 , SER B:311 , GLY B:313 , THR B:314 , VAL B:317 , GOL B:1007 , HOH B:2130 , HOH B:2175 , HOH B:2176 , HOH B:2177BINDING SITE FOR RESIDUE TYD B 1004
7AC7SOFTWAREGLY B:12 , ASP B:13 , PRO B:126 , SER B:311 , ALA B:312 , ASP B:333 , K B:417 , TYD B:1004 , BGC D:8BINDING SITE FOR RESIDUE GOL B 1007
8AC8SOFTWARECYS A:8 , GLY A:9 , THR A:10 , ASP A:13 , LEU A:55 , MET A:60 , LEU A:61 , GLN A:62 , MET A:65 , PRO A:66 , PRO A:67 , PRO A:68 , GLU A:73 , LEU A:76 , THR A:80 , GLY A:102 , ASP A:103 , ASP A:141 , PRO A:143 , TYR A:166 , ASN A:331 , THR A:332 , GOL A:1006 , HOH A:2024 , HOH A:2090 , HOH A:2134 , HOH C:2001 , HOH C:2002 , HOH C:2003 , HOH C:2005 , HOH C:2006 , HOH C:2009 , HOH C:2010 , HOH C:2011 , HOH C:2012 , HOH C:2013BINDING SITE FOR CHAIN C OF DESVANCOSAMINYL VANCOMYCIN
9AC9SOFTWARECYS B:8 , GLY B:9 , ASP B:13 , LEU B:55 , MET B:60 , LEU B:61 , GLN B:62 , MET B:65 , PRO B:66 , PRO B:67 , PRO B:68 , LEU B:76 , THR B:80 , GLY B:102 , ASP B:103 , ASP B:141 , PRO B:143 , ARG B:165 , TYR B:166 , ASN B:331 , GOL B:1007 , HOH B:2024 , HOH D:2001 , HOH D:2002 , HOH D:2003 , HOH D:2004 , HOH D:2005 , HOH D:2006 , HOH D:2007BINDING SITE FOR CHAIN D OF DESVANCOSAMINYL VANCOMYCIN

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ghp C:5 -Omy C:6
2Ghp D:5 -Omy D:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RRV)

(-) 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:401
 aligned with GTFD_AMYOR | Q9AFC7 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:401
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400 
           GTFD_AMYOR     1 MRVLLSVCGTRGDVEIGVALADRLKALGVQTRMCAPPAAEERLAEVGVPHVPVGLPQHMMLQEGMPPPPPEEEQRLAAMTVEMQFDAVPGAAEGCAAVVAVGDLAAATGVRSVAEKLGLPFFYSVPSPVYLASPHLPPAYDEPTTPGVTDIRVLWEERAARFADRYGPTLNRRRAEIGLPPVEDVFGYGHGERPCWPADPVLAPLQPDVDAVQTGAWLLSDERPLPPELEAFLAAGSPPVHIGFGSSSGRGIADAAKVAVEAIRAQGRRVILSRGWTELVLPDDRDDCFAIDEVNFQALFRRVAAVIHHGSAGTEHVATRAGVPQLVIPRNTDQPYFAGRVAALGIGVAHDGPTPTFESLSAALTTVLAPETRARAEAVAGMVLTDGAAAAADLVLAAVGR 401
               SCOP domains d1rrva_ A: TDP-vancosaminyltransferase GftD                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1rrvA01 A:1-217,A:384-401 Glycogen Phosphorylase B;                                                                                                                                                                      1rrvA02 A:218-383 Glycogen Phosphorylase B;                                                                                                                           1rrvA01            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh..eee...hhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh..eeeee.hhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.....ee.............................hhhhhhhhhh....eee......hhhhhhhhhhhhhhhhhh...eeee..............eeee...hhhhhhhhh.eeee..hhhhhhhhhhhh..eee.....hhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rrv A   1 MRVLLSVCGTRGDVEIGVALADRLKALGVQTRMCAPPAAEERLAEVGVPHVPVGLPQHMMLQEGMPPPPPEEEQRLAAMTVEMQFDAVPGAAEGCAAVVAVGDLAAATGVRSVAEKLGLPFFYSVPSPVYLASPHLPPAYDEPTTPGVTDIRVLWEERAARFADRYGPTLNRRRAEIGLPPVEDVFGYGHGERPLLAADPVLAPLQPDVDAVQTGAWLLSDERPLPPELEAFLAAGSPPVHIGFGSSSGRGIADAAKVAVEAIRAQGRRVILSRGWTELVLPDDRDDCFAIDEVNFQALFRRVAAVIHHGSAGTEHVATRAGVPQLVIPRNTDQPYFAGRVAALGIGVAHDGPTPTFESLSAALTTVLAPETRARAEAVAGMVLTDGAAAAADLVLAAVGR 401
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400 


Chain B from PDB  Type:PROTEIN  Length:400
 aligned with GTFD_AMYOR | Q9AFC7 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:400
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
           GTFD_AMYOR     1 MRVLLSVCGTRGDVEIGVALADRLKALGVQTRMCAPPAAEERLAEVGVPHVPVGLPQHMMLQEGMPPPPPEEEQRLAAMTVEMQFDAVPGAAEGCAAVVAVGDLAAATGVRSVAEKLGLPFFYSVPSPVYLASPHLPPAYDEPTTPGVTDIRVLWEERAARFADRYGPTLNRRRAEIGLPPVEDVFGYGHGERPCWPADPVLAPLQPDVDAVQTGAWLLSDERPLPPELEAFLAAGSPPVHIGFGSSSGRGIADAAKVAVEAIRAQGRRVILSRGWTELVLPDDRDDCFAIDEVNFQALFRRVAAVIHHGSAGTEHVATRAGVPQLVIPRNTDQPYFAGRVAALGIGVAHDGPTPTFESLSAALTTVLAPETRARAEAVAGMVLTDGAAAAADLVLAAVG 400
               SCOP domains d1rrvb_ B: TDP-vancosaminyltransferase GftD                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1rrvB01 B:1-217,B:384-400 Glycogen Phosphorylase B;                                                                                                                                                                      1rrvB02 B:218-383 Glycogen Phosphorylase B;                                                                                                                           1rrvB01           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh..eee...hhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhh...eeeee.hhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.....ee.............................hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh...eeee..............eeee...hhhhhh....eeee..hhhhhhhhhhh...eee.....hhhhhhhhhhhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rrv B   1 MRVLLSVCGTRGDVEIGVALADRLKALGVQTRMCAPPAAEERLAEVGVPHVPVGLPQHMMLQEGMPPPPPEEEQRLAAMTVEMQFDAVPGAAEGCAAVVAVGDLAAATGVRSVAEKLGLPFFYSVPSPVYLASPHLPPAYDEPTTPGVTDIRVLWEERAARFADRYGPTLNRRRAEIGLPPVEDVFGYGHGERPLLAADPVLAPLQPDVDAVQTGAWLLSDERPLPPELEAFLAAGSPPVHIGFGSSSGRGIADAAKVAVEAIRAQGRRVILSRGWTELVLPDDRDDCFAIDEVNFQALFRRVAAVIHHGSAGTEHVATRAGVPQLVIPRNTDQPYFAGRVAALGIGVAHDGPTPTFESLSAALTTVLAPETRARAEAVAGMVLTDGAAAAADLVLAAVG 400
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400


Chain C 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
                 1rrv C   1 xxNxxxx   7
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG


Chain D 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
                 1rrv D   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GTFD_AMYOR | Q9AFC7)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016758    transferase activity, transferring hexosyl groups    Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0030259    lipid glycosylation    Covalent attachment of a glycosyl residue to a lipid molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0033072    vancomycin biosynthetic process    The chemical reactions and pathways leading to the formation of vancomycin, (3S,6R,7R,11R,23S,26S,30aS,36R,38aR)-44-[2-O-(3-amino-2,3,6-trideoxy-3-C-methyl-alpha-L-lyxo-hexopyranosyl)-beta-D-glucopyranosyloxy]-3-(carbamoylmethyl)-10,19-dichloro-2,3,4,5,6,7,23,25,26,36,37,38,38a-tetradecahydro-7,22,28,30,32-pentahydroxy-6-(N-methyl-D-leucyl)-2,5,24,38,39-pentaoxo-1H,22H-23,36-(epiminomethano)-8,11:18,21-dietheno-13,16:31,35-di(metheno)[1,6,9]oxadiazacyclohexadecino[4,5-m][10,2,16]benzoxadiazacyclotetracosine-26-carboxylic acid, a complex glycopeptide from Streptomyces orientalis that inhibits a specific step in the synthesis of the peptidoglycan layer in Gram-positive bacteria.

 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 ]
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GHP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OMY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OMZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TYD  [ 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 ]
 
  Cis Peptide Bonds
    Ghp C:5 - Omy C:6   [ RasMol ]  
    Ghp D:5 - Omy D: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
  1rrv
    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
  GTFD_AMYOR | Q9AFC7
    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
  GTFD_AMYOR | Q9AFC7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) 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
1qd8 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL GLYCIN
1sho CRYSTAL STRUCTURE OF VANCOMYCIN