1AA5 - JenaLib

Title :   VANCOMYCIN

Authors :   P. J. Loll, A. E. Bevivino, B. D. Korty, P. H. Axelsen

Date :   23 Jan 97 (Deposition) - 20 Aug 97 (Release) - 19 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.89

Chains :   Asym. Unit : A,B
Biol. Unit 1: A (1x),B (1x)

Keywords :   Glycopeptide, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. Loll, A. E. Bevivino, B. D. Korty, P. H. Axelsen
Simultaneous Recognition Of A Carboxylate-Containing Ligand And An Intramolecular Surrogate Ligand In The Crystal Structure Of An Asymmetric Vancomycin Dimer.
J. Am. Chem. Soc. V. 119 1516 1997
PubMed: search | Reference-DOI: 10.1021/JA963566P

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 21)

Asymmetric Unit (9, 21)

No.	Name	Count	Type	Full Name
1	3FG	2	Mod. Amino Acid	(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2	ACY	1	Ligand/Ion	ACETIC ACID
3	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
4	CL	4	Ligand/Ion	CHLORIDE ION
5	GHP	4	Mod. Amino Acid	(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6	MLU	2	Mod. Amino Acid	N-METHYL-D-LEUCINE
7	OMY	2	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8	OMZ	2	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9	RER	2	Ligand/Ion	(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE

Biological Unit 1 (8, 9)

No.	Name	Count	Type	Full Name
1	3FG	1	Mod. Amino Acid	(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2	ACY	1	Ligand/Ion	ACETIC ACID
3	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	GHP	2	Mod. Amino Acid	(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6	MLU	1	Mod. Amino Acid	N-METHYL-D-LEUCINE
7	OMY	1	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
8	OMZ	1	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
9	RER	1	Ligand/Ion	(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:2033 , HOH A:2034 , MLU B:1 , OMZ B:2 , ASN B:3 , GHP B:4	BINDING SITE FOR RESIDUE ACY A 11
2	AC2	SOFTWARE	ASN A:3 , OMY A:6 , 3FG A:7 , OMZ B:2	BINDING SITE FOR RESIDUE CL A 21
3	AC3	SOFTWARE	MLU A:1 , OMZ A:2 , HOH A:2003 , HOH A:2005	BINDING SITE FOR RESIDUE CL A 22
4	AC4	SOFTWARE	OMZ A:2 , RER A:9 , MLU B:1 , RER B:9	BINDING SITE FOR RESIDUE CL B 21
5	AC5	SOFTWARE	OMY B:6 , 3FG B:7 , HOH B:2006	BINDING SITE FOR RESIDUE CL B 22
6	AC6	SOFTWARE	CL A:21 , CL A:22 , HOH A:2001 , HOH A:2002 , HOH A:2009 , HOH A:2010 , HOH A:2015 , HOH A:2016 , HOH A:2017 , HOH A:2018 , HOH A:2019 , HOH A:2021 , HOH A:2022 , HOH A:2023 , HOH A:2024 , HOH A:2025 , HOH A:2026 , HOH A:2027 , HOH A:2029 , HOH A:2030 , HOH A:2031 , HOH A:2032 , 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:9 , CL B:21 , HOH B:2001 , HOH B:2007 , HOH B:2017 , HOH B:2018	BINDING SITE FOR CHAIN A OF VANCOMYCIN
7	AC7	SOFTWARE	MLU 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 , ACY A:11 , CL A:21 , HOH A:2001 , HOH A:2026 , HOH A:2030 , CL B:21 , CL B:22 , HOH B:2001 , HOH B:2002 , HOH B:2003 , HOH B:2006 , HOH B:2007 , HOH B:2008 , HOH B:2009 , HOH B:2010 , HOH B:2011 , HOH B:2012 , HOH B:2013 , HOH B:2015 , HOH B:2017 , HOH B:2018 , HOH B:2019 , HOH B:2020	BINDING SITE FOR CHAIN B OF VANCOMYCIN

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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
                   1aa5 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
                   1aa5 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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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 ]
		ACY	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ghp A:5 - Omy A:6	[ RasMol ]
		Ghp B:5 - Omy B:6	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	1aa5
		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)

Related Entries Specified in the PDB File

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

Description