1GHG - JenaLib

Title :   CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON

Authors :   J. Kaplan, B. D. Korty, P. H. Axelsen, P. J. Loll

Date :   13 Dec 00 (Deposition) - 12 Feb 01 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.98

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

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

Reference :   J. Kaplan, B. D. Korty, P. H. Axelsen, P. J. Loll
The Role Of Sugar Residues In Molecular Recognition By Vancomycin
J. Med. Chem. V. 44 1837 2001
PubMed-ID: 11356118 | Reference-DOI: 10.1021/JM0005306

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 30)

Asymmetric Unit (7, 30)

No.	Name	Count	Type	Full Name
1	3FG	4	Mod. Amino Acid	(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2	ACY	4	Ligand/Ion	ACETIC ACID
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	GHP	8	Mod. Amino Acid	(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
5	MLU	4	Mod. Amino Acid	N-METHYLLEUCINE
6	OMY	4	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
7	OMZ	4	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE

Biological Unit 1 (6, 14)

No.	Name	Count	Type	Full Name
1	3FG	2	Mod. Amino Acid	(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2	ACY	2	Ligand/Ion	ACETIC ACID
3	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
4	GHP	4	Mod. Amino Acid	(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
5	MLU	2	Mod. Amino Acid	N-METHYLLEUCINE
6	OMY	2	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
7	OMZ	2	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE

Biological Unit 2 (7, 16)

No.	Name	Count	Type	Full Name
1	3FG	2	Mod. Amino Acid	(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2	ACY	2	Ligand/Ion	ACETIC ACID
3	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
4	GHP	4	Mod. Amino Acid	(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
5	MLU	2	Mod. Amino Acid	N-METHYLLEUCINE
6	OMY	2	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
7	OMZ	2	Mod. Amino Acid	(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MLU A:1 , OMZ A:2 , ASN A:3 , GHP A:4 , OMY A:6 , MLU B:1	BINDING SITE FOR RESIDUE ACY A 11
02	AC2	SOFTWARE	MLU B:1 , OMZ B:2 , ASN B:3 , GHP B:4 , GHP C:4 , OMY C:6 , HOH D:2005	BINDING SITE FOR RESIDUE ACY B 11
03	AC3	SOFTWARE	MLU C:1 , OMZ C:2 , ASN C:3 , GHP C:4 , DMS C:12 , HOH C:2013 , 3FG D:7	BINDING SITE FOR RESIDUE ACY C 11
04	AC4	SOFTWARE	GHP C:4 , GHP C:5 , OMY C:6 , 3FG C:7 , ACY C:11	BINDING SITE FOR RESIDUE DMS C 12
05	AC5	SOFTWARE	3FG C:7 , MLU D:1 , OMZ D:2 , ASN D:3 , GHP D:4 , HOH D:2006	BINDING SITE FOR RESIDUE ACY D 11
06	AC6	SOFTWARE	OMZ B:2 , GHP B:4 , GHP D:5 , OMY D:6 , 3FG D:7	BINDING SITE FOR RESIDUE DMS D 12
07	AC7	SOFTWARE	ACY A:11 , HOH A:2001 , HOH A:2005 , HOH A:2007 , HOH A:2008 , HOH A:2009 , HOH A:2011 , HOH A:2012 , HOH A:2013 , HOH A:2014 , HOH A:2015 , HOH A:2016 , HOH A:2017 , HOH A:2018 , MLU B:1 , OMZ B:2 , ASN B:3 , GHP B:4 , GHP B:5 , OMY B:6 , 3FG B:7 , HOH B:2011 , MLU C:1 , OMZ C:2 , ASN C:3 , GHP C:5 , 3FG C:7 , HOH C:2013 , MLU D:1 , OMY D:6 , HOH D:2003 , HOH D:2007 , HOH D:2010	BINDING SITE FOR CHAIN A OF VANCOMYCIN AGLYCONE
08	AC8	SOFTWARE	MLU A:1 , OMZ A:2 , ASN A:3 , GHP A:4 , GHP A:5 , OMY A:6 , 3FG A:7 , ACY A:11 , HOH A:2007 , HOH A:2013 , HOH A:2016 , ACY B:11 , HOH B:2001 , HOH B:2004 , HOH B:2005 , HOH B:2007 , HOH B:2008 , HOH B:2011 , HOH B:2012 , HOH B:2013 , HOH B:2014 , HOH B:2015 , MLU C:1 , OMZ C:2 , GHP C:4 , GHP C:5 , OMY C:6 , MLU D:1 , OMZ D:2 , ASN D:3 , GHP D:4 , GHP D:5 , 3FG D:7 , DMS D:12 , HOH D:2003 , HOH D:2005 , HOH D:2006	BINDING SITE FOR CHAIN B OF VANCOMYCIN AGLYCONE
09	AC9	SOFTWARE	MLU A:1 , ASN A:3 , GHP A:4 , GHP A:5 , OMY A:6 , 3FG A:7 , MLU B:1 , OMZ B:2 , GHP B:4 , OMY B:6 , 3FG B:7 , ACY B:11 , ACY C:11 , DMS C:12 , HOH C:2001 , HOH C:2002 , HOH C:2005 , HOH C:2007 , HOH C:2008 , HOH C:2010 , HOH C:2013 , HOH C:2014 , HOH C:2015 , HOH C:2016 , HOH C:2017 , HOH C:2018 , HOH C:2019 , MLU D:1 , ASN D:3 , GHP D:4 , GHP D:5 , OMY D:6 , 3FG D:7 , ACY D:11 , HOH D:2001	BINDING SITE FOR CHAIN C OF VANCOMYCIN AGLYCONE
10	BC1	SOFTWARE	GHP A:4 , GHP A:5 , OMY A:6 , HOH A:2017 , MLU B:1 , OMZ B:2 , ASN B:3 , GHP B:4 , GHP B:5 , 3FG B:7 , HOH B:2001 , HOH B:2004 , HOH B:2007 , HOH B:2015 , MLU C:1 , OMZ C:2 , ASN C:3 , GHP C:4 , GHP C:5 , OMY C:6 , 3FG C:7 , ACY C:11 , HOH C:2005 , HOH C:2010 , ACY D:11 , DMS D:12 , HOH D:2001 , HOH D:2002 , HOH D:2003 , HOH D:2004 , HOH D:2005 , HOH D:2006 , HOH D:2007 , HOH D:2010 , HOH D:2011 , HOH D:2012 , HOH D:2013 , HOH D:2014 , HOH D:2015	BINDING SITE FOR CHAIN D OF VANCOMYCIN AGLYCONE

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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

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

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1aa5	CRYSTAL STRUCTURE OF VANCOMYCIN
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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
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

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