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(-) Description

Title :  COMPLEX OF VANCOMYCIN WITH DI-ACETYL-LYS-D-ALA-D-ALA
 
Authors :  Y. Nitanai, K. Kakoi, K. Aoki
Date :  20 Sep 00  (Deposition) - 01 Nov 00  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,G  (1x)
Biol. Unit 2:  B,H  (1x)
Biol. Unit 3:  C,I  (1x)
Biol. Unit 4:  D,J  (1x)
Biol. Unit 5:  E,K  (1x)
Biol. Unit 6:  F,L  (1x)
Keywords :  Peptide-Antibiotic Complex, Glycopeptide, Antibiotic, Vancomycin, Cell Wall Precursor, Structural Protein-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Nitanai, T. Kikuchi, K. Kakoi, S. Hanamaki, I. Fujisawa, K. Aoki
Crystal Structures Of The Complexes Between Vancomycin And Cell-Wall Precursor Analogs.
J. Mol. Biol. V. 385 1422 2009
PubMed-ID: 18976660  |  Reference-DOI: 10.1016/J.JMB.2008.10.026

(-) Compounds

Molecule 1 - VANCOMYCIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958
    Other Details: SEQUENCE OCCURS IN NOCARDIA ORIENTALIS
    Synthetic: YES
 
Molecule 2 - DI-ACETYL-LYS-D-ALA-D-ALA
    Chains: G, H, I, J, K, L
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): A     G     
Biological Unit 2 (1x):  B     H    
Biological Unit 3 (1x):   C     I   
Biological Unit 4 (1x):    D     J  
Biological Unit 5 (1x):     E     K 
Biological Unit 6 (1x):      F     L

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 66)

Asymmetric Unit (9, 66)
No.NameCountTypeFull Name
13FG6Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC6Ligand/IonBETA-D-GLUCOSE
3DAL12OTHERD-ALANINE
4DLS6OTHERDI-ACETYL-LYSINE
5GHP12Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6MLU6Mod. Amino AcidN-METHYLLEUCINE
7OMY6Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8OMZ6Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9RER6Ligand/Ion(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
Biological Unit 1 (9, 11)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3DAL2OTHERD-ALANINE
4DLS1OTHERDI-ACETYL-LYSINE
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 (9, 11)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3DAL2OTHERD-ALANINE
4DLS1OTHERDI-ACETYL-LYSINE
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 3 (9, 11)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3DAL2OTHERD-ALANINE
4DLS1OTHERDI-ACETYL-LYSINE
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 4 (9, 11)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3DAL2OTHERD-ALANINE
4DLS1OTHERDI-ACETYL-LYSINE
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 5 (9, 11)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3DAL2OTHERD-ALANINE
4DLS1OTHERDI-ACETYL-LYSINE
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 6 (9, 11)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3DAL2OTHERD-ALANINE
4DLS1OTHERDI-ACETYL-LYSINE
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

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2001 , HOH A:2005 , HOH A:2006 , HOH A:2007 , HOH A:2008 , HOH A:2009 , HOH A:2010 , HOH A:2011 , HOH A:2012 , HOH A:2013 , HOH A:2014 , HOH A:2015 , HOH A:2017 , HOH A:2018 , HOH A:2019 , HOH A:2020 , ASN B:3 , GHP B:4 , GHP B:5 , OMY B:6 , BGC B:8 , RER B:9 , HOH B:2004 , HOH B:2008 , HOH B:2015 , GHP C:5 , MLU D:1 , OMZ D:2 , ASN D:3 , GHP D:5 , 3FG D:7 , MLU E:1 , BGC E:8 , HOH E:2001 , HOH E:2020 , MLU F:1 , BGC F:8 , RER F:9 , DLS G:1 , DAL G:2 , DAL G:3 , HOH G:2002 , DLS J:1BINDING SITE FOR CHAIN A OF VANCOMYCIN
2AC2SOFTWAREOMZ A:2 , ASN A:3 , GHP A:4 , GHP A:5 , OMY A:6 , BGC A:8 , RER A:9 , HOH A:2006 , HOH B:2002 , HOH B:2003 , HOH B:2004 , HOH B:2007 , HOH B:2008 , HOH B:2009 , HOH B:2010 , HOH B:2011 , HOH B:2012 , HOH B:2013 , HOH B:2014 , HOH B:2015 , MLU C:1 , MLU D:1 , OMY D:6 , 3FG D:7 , RER D:9 , HOH D:2008 , HOH D:2009 , HOH E:2004 , MLU F:1 , OMZ F:2 , ASN F:3 , GHP F:5 , 3FG F:7 , DLS H:1 , DAL H:2 , DAL H:3 , DLS J:1BINDING SITE FOR CHAIN B OF VANCOMYCIN
3AC3SOFTWARE3FG A:7 , HOH A:2012 , MLU B:1 , HOH B:2014 , HOH C:2003 , HOH C:2004 , HOH C:2006 , HOH C:2008 , HOH C:2009 , HOH C:2010 , HOH C:2011 , HOH C:2012 , HOH C:2013 , HOH C:2014 , OMZ D:2 , ASN D:3 , GHP D:4 , GHP D:5 , OMY D:6 , BGC D:8 , RER D:9 , HOH D:2005 , HOH D:2008 , GHP E:5 , 3FG E:7 , HOH E:2013 , HOH E:2019 , HOH E:2021 , 3FG F:7 , DLS H:1 , DLS I:1 , DAL I:2 , DAL I:3 , DLS K:1 , HOH K:2001BINDING SITE FOR CHAIN C OF VANCOMYCIN
4AC4SOFTWAREMLU A:1 , ASN A:3 , GHP A:4 , GHP A:5 , 3FG A:7 , RER A:9 , HOH A:2012 , GHP B:5 , OMY B:6 , 3FG B:7 , RER B:9 , HOH B:2014 , OMZ C:2 , ASN C:3 , GHP C:4 , GHP C:5 , OMY C:6 , BGC C:8 , HOH C:2010 , HOH C:2012 , HOH D:2001 , HOH D:2003 , HOH D:2004 , HOH D:2005 , HOH D:2007 , HOH D:2008 , HOH D:2009 , HOH D:2010 , HOH D:2011 , HOH D:2012 , HOH D:2013 , MLU E:1 , OMZ E:2 , ASN E:3 , HOH E:2003 , HOH E:2004 , MLU F:1 , GHP F:5 , OMY F:6 , 3FG F:7 , DAL G:2 , HOH G:2002 , DLS J:1 , DAL J:2 , DAL J:3 , DLS L:1 , DAL L:3BINDING SITE FOR CHAIN D OF VANCOMYCIN
5AC5SOFTWAREMLU A:1 , ASN A:3 , RER A:9 , HOH A:2014 , HOH A:2019 , HOH B:2010 , MLU C:1 , OMZ C:2 , RER C:9 , HOH C:2003 , OMZ D:2 , RER D:9 , HOH D:2003 , HOH E:2001 , HOH E:2003 , HOH E:2004 , HOH E:2006 , HOH E:2007 , HOH E:2008 , HOH E:2010 , HOH E:2011 , HOH E:2012 , HOH E:2013 , HOH E:2015 , HOH E:2017 , HOH E:2018 , HOH E:2019 , HOH E:2020 , HOH E:2021 , OMZ F:2 , ASN F:3 , GHP F:4 , GHP F:5 , OMY F:6 , BGC F:8 , RER F:9 , DLS K:1 , DAL K:2 , DAL K:3 , DLS L:1BINDING SITE FOR CHAIN E OF VANCOMYCIN
6AC6SOFTWAREGHP A:5 , 3FG A:7 , HOH A:2009 , HOH A:2011 , MLU B:1 , ASN B:3 , GHP B:4 , GHP B:5 , 3FG B:7 , HOH B:2003 , RER C:9 , MLU D:1 , 3FG D:7 , RER D:9 , HOH D:2007 , OMZ E:2 , ASN E:3 , GHP E:4 , GHP E:5 , OMY E:6 , BGC E:8 , RER E:9 , HOH E:2003 , HOH E:2017 , HOH F:2001 , HOH F:2002 , HOH F:2003 , HOH F:2004 , HOH F:2006 , HOH F:2007 , HOH F:2008 , HOH F:2009 , HOH F:2010 , HOH F:2011 , HOH F:2012 , HOH F:2013 , HOH F:2014 , DLS G:1 , DAL H:2 , DLS J:1 , DAL J:3 , DLS L:1 , DAL L:2 , DAL L:3 , HOH L:2002BINDING SITE FOR CHAIN F OF VANCOMYCIN

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ghp A:5 -Omy A:6
2Ghp B:5 -Omy B:6
3Ghp C:5 -Omy C:6
4Ghp D:5 -Omy D:6
5Ghp E:5 -Omy E:6
6Ghp F:5 -Omy F:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1FVM)

(-) 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
                   1fvm 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
                   1fvm B 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG


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
                   1fvm 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
                   1fvm D 1 xxNxxxx 7
                            || ||||
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG


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


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


Chain G from PDB  Type:OTHER  Length:3
                                 
                   1fvm G 1 xxx 3
                            |||
                            |||
                            1-DLS
                             2-DAL
                              3-DAL


Chain H from PDB  Type:OTHER  Length:3
                                 
                   1fvm H 1 xxx 3
                            |||
                            |||
                            1-DLS
                             2-DAL
                              3-DAL


Chain I from PDB  Type:OTHER  Length:3
                                 
                   1fvm I 1 xxx 3
                            |||
                            |||
                            1-DLS
                             2-DAL
                              3-DAL


Chain J from PDB  Type:OTHER  Length:3
                                 
                   1fvm J 1 xxx 3
                            |||
                            |||
                            1-DLS
                             2-DAL
                              3-DAL


Chain K from PDB  Type:OTHER  Length:3
                                 
                   1fvm K 1 xxx 3
                            |||
                            |||
                            1-DLS
                             2-DAL
                              3-DAL


Chain L from PDB  Type:OTHER  Length:3
                                 
                   1fvm L 1 xxx 3
                            |||
                            |||
                            1-DLS
                             2-DAL
                              3-DAL
   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 1FVM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  1fvm
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 Related Entries

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(-) 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
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
1rrv CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEXED WITH TDP AND DESVANCOSAMINYL VANCOMYCIN.
1sho CRYSTAL STRUCTURE OF VANCOMYCIN