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239,267
Structures from the PDB archive

1,068,577
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QUERY: BIRD Type = "Glycopeptide"

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Search Summary

This query matches 47 Structures.

Refinements

Structure Determination Methodology

experimental (47)

Scientific Name of Source Organism

	Amycolatopsis orientalis (15)
	Actinoplanes teichomyceticus (9)
	Homo sapiens (5)
	Amycolatopsis sp. (4)
	uncultured actinomycete (4)
	Staphylococcus aureus (3)
	Tequatrovirus T4 (3)
	Eleftheria terrae (2)
	Nonomuraea gerenzanensis (2)
	synthetic construct (2)

More...

Taxonomy

	Bacteria (42)
	Eukaryota (6)
	Duplodnaviria (3)
	other sequences (2)

Experimental Method

	X-RAY DIFFRACTION (42)
	ELECTRON CRYSTALLOGRAPHY (2)
	SOLID-STATE NMR (2)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (47)

Refinement Resolution (Å)

	0.5 - 1.0 (6)
	1.0 - 1.5 (12)
	1.5 - 2.0 (9)
	2.0 - 2.5 (10)
	2.5 - 3.0 (6)
	3.5 - 4.0 (1)

Release Date

	1985 - 1989 (1)
	1995 - 1999 (6)
	2000 - 2004 (9)
	2005 - 2009 (6)
	2010 - 2014 (15)
	2015 - 2019 (5)
	2020 - 2024 (5)

Enzyme Classification Name

	Hydrolases (12)
	Transferases (8)
	Ligases (2)

Membrane Protein Annotation

	MemProtMD (1)
	PDBTM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (22)
	Cyclic (8)

SCOP Classification

	Alpha and beta proteins (a+b) (11)
	Alpha and beta proteins (a/b) (5)
	Artifacts (1)

AllSelected

1 to 25 of 47 Structures

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1AA5 \| pdb_00001aa5	Download File View File

VANCOMYCIN

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

(1997) J Am Chem Soc 119: 1516

Released	1997-08-20
Method	X-RAY DIFFRACTION 0.89 Å
Organisms	Amycolatopsis orientalis
Macromolecule	VANCOMYCIN (protein)
Unique Ligands	ACY, CL
Unique branched monosaccharides	BGC, RER

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1C0Q \| pdb_00001c0q	Download File View File

COMPLEX OF VANCOMYCIN WITH 2-ACETOXY-D-PROPANOIC ACID

Loll, P.J., Kaplan, J., Selinsky, B., Axelsen, P.H.

(1999) J Med Chem 42: 4714-4719

Released	1999-07-30
Method	X-RAY DIFFRACTION 1 Å
Organisms	Amycolatopsis orientalis
Macromolecule	VANCOMYCIN (protein)
Unique Ligands	CL, LAC
Unique branched monosaccharides	BGC, RER

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1C0R \| pdb_00001c0r	Download File View File

COMPLEX OF VANCOMYCIN WITH D-LACTIC ACID

Loll, P.J., Kaplan, J., Selinsky, B., Axelsen, P.H.

(1999) J Med Chem 42: 4714

Released	1999-07-30
Method	X-RAY DIFFRACTION 1 Å
Organisms	Amycolatopsis orientalis
Macromolecule	VANCOMYCIN (protein)
Unique Ligands	CL, LAC
Unique branched monosaccharides	BGC, RER

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1DMT \| pdb_00001dmt	Download File View File

STRUCTURE OF HUMAN NEUTRAL ENDOPEPTIDASE COMPLEXED WITH PHOSPHORAMIDON

Oefner, C., D'Arcy, A., Hennig, M., Winkler, F.K., Dale, G.E.

(2000) J Mol Biology 296: 341-349

Released	2000-12-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	NEUTRAL ENDOPEPTIDASE (protein)
Unique Ligands	GOL, NAG, RDF, ZN

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1FVM \| pdb_00001fvm	Download File View File

Complex of vancomycin with DI-acetyl-LYS-D-ALA-D-ALA

Nitanai, Y., Kakoi, K., Aoki, K.

(2009) J Mol Biology 385: 1422

Released	2000-11-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Amycolatopsis orientalis
Macromolecule	DI-ACETYL-LYS-D-ALA-D-ALA (protein) VANCOMYCIN (protein)
Unique branched monosaccharides	BGC, RER

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1GAC \| pdb_00001gac	Download File View File

NMR structure of asymmetric homodimer of a82846b, a glycopeptide antibiotic, complexed with its cell wall pentapeptide fragment

Kline, A.D., Prowse, W.G., Skelton, M.A., Loncharich, R.J.

(1995) Biochemistry 34: 9632

Released	1996-08-17
Method	SOLUTION NMR
Organisms	Amycolatopsis orientalis
Macromolecule	CELL WALL PENTAPEPTIDE (protein) CHLOROORIENTICIN A (protein)
Unique Ligands	RER
Unique branched monosaccharides	BGC, RER

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1GO6 \| pdb_00001go6	Download File View File

Balhimycin in complex with Lys-D-ala-D-ala

Lehmann, C., Bunkoczi, G., Vertesy, L., Sheldrick, G.M.

(2002) J Mol Biology 318: 723

Released	2002-06-13
Method	X-RAY DIFFRACTION 0.98 Å
Organisms	Amycolatopsis sp. synthetic construct
Macromolecule	BALHIMYCIN (protein) PEPTIDE LYS-DAL-DAL (protein)
Unique Ligands	BGC, CIT, DVC, MPD, MRD

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1HH3 \| pdb_00001hh3	Download File View File

Decaplanin first P21-Form

Lehmann, C., Vertessy, L., Sheldrick, G.M., Dauter, Z., Dauter, M.

(2003) Helvetica Chim Acta 86: 1478

Released	2005-07-11
Method	X-RAY DIFFRACTION 1 Å
Organisms	uncultured actinomycete
Macromolecule	DECAPLANIN (protein)
Unique Ligands	ERE, GOL
Unique branched monosaccharides	BGC, RAM

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1HHA \| pdb_00001hha	Download File View File

Decaplanin first P6122-Form

Lehmann, C., Vertessy, L., Sheldrick, G.M., Dauter, Z., Dauter, M.

(2003) Helvetica Chim Acta 86: 1478

Released	2005-07-11
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	uncultured actinomycete
Macromolecule	DECAPLANIN (protein)
Unique Ligands	ERE, GOL
Unique branched monosaccharides	BGC, RAM

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1HHC \| pdb_00001hhc	Download File View File

Crystal structure of Decaplanin - space group P21, second form

Lehmann, C., Vertessy, L., Sheldrick, G.M., Dauter, Z., Dauter, M.

(2003) Helvetica Chim Acta 86: 1478

Released	2005-07-11
Method	X-RAY DIFFRACTION 1.13 Å
Organisms	uncultured actinomycete
Macromolecule	DECAPLANIN (protein)
Unique Ligands	CIT, ERE
Unique branched monosaccharides	BGC, RAM

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1HHF \| pdb_00001hhf	Download File View File

Decaplanin second P6122-Form

Lehmann, C., Vertessy, L., Sheldrick, G.M., Dauter, Z., Dauter, M.

(2003) Helvetica Chim Acta 86: 1478

Released	2005-07-11
Method	X-RAY DIFFRACTION 1.47 Å
Organisms	uncultured actinomycete
Macromolecule	DECAPLANIN (protein)
Unique Ligands	CL, ERE, PO4
Unique branched monosaccharides	BGC, RAM

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1HHU \| pdb_00001hhu	Download File View File

Balhimycin in complex with D-Ala-D-Ala

Lehmann, C., Bunkoczi, G., Sheldrick, G.M., Vertessy, L.

(2002) J Mol Biology 318: 723

Released	2003-09-05
Method	X-RAY DIFFRACTION 0.89 Å
Organisms	Amycolatopsis sp.
Macromolecule	BALHIMYCIN (protein)
Unique Ligands	BGC, CIT, DAL, DVC, MPD

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1HHY \| pdb_00001hhy	Download File View File

Deglucobalhimycin in complex with D-Ala-D-Ala

Lehmann, C., Bunkoczi, G., Sheldrick, G.M., Vertesy, L.

(2002) J Mol Biology 318: 723

Released	2003-09-05
Method	X-RAY DIFFRACTION 0.89 Å
Organisms	Amycolatopsis sp.
Macromolecule	DEGLUCOBALHIMYCIN (protein)
Unique Ligands	DAL, DVC, NA, PGO

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1HHZ \| pdb_00001hhz	Download File View File

Deglucobalhimycin in complex with cell wall pentapeptide

Lehmann, C., Bunkoczi, G., Sheldrick, G.M., Vertesy, L.

(2002) J Mol Biology 318: 723

Released	2003-09-05
Method	X-RAY DIFFRACTION 0.99 Å
Organisms	Amycolatopsis sp. synthetic construct
Macromolecule	CELL WALL PEPTIDE (protein) DEGLUCOBALHIMYCIN (protein)
Unique Ligands	DVC, PGR

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1PN3 \| pdb_00001pn3	Download File View File

Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV.

Mulichak, A.M., Losey, H.C., Lu, W., Wawrzak, Z., Walsh, C.T., Garavito, R.M.

(2003) Proc Natl Acad Sci U S A 100: 9238

Released	2003-08-12
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Amycolatopsis orientalis
Macromolecule	DESVANCOSAMINYL VANCOMYCIN (protein) GLYCOSYLTRANSFERASE GTFA (protein)
Unique Ligands	BGC, TYD

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1PNV \| pdb_00001pnv	Download File View File

Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and Vancomycin

Mulichak, A.M., Losey, H.C., Lu, W., Wawrzak, Z., Walsh, C.T., Garavito, R.M.

(2003) Proc Natl Acad Sci U S A 100: 9238

Released	2003-08-12
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Amycolatopsis orientalis
Macromolecule	GLYCOSYLTRANSFERASE GTFA (protein) VANCOMYCIN (protein)
Unique Ligands	TYD
Unique branched monosaccharides	BGC, RER

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1QD8 \| pdb_00001qd8	Download File View File

COMPLEX OF VANCOMYCIN WITH N-ACETYL GLYCINE

Loll, P.J., Kaplan, J., Selinsky, B., Axelsen, P.H.

(1999) J Med Chem 42: 4714

Released	1999-08-16
Method	X-RAY DIFFRACTION 1 Å
Organisms	Amycolatopsis orientalis
Macromolecule	VANCOMYCIN (protein)
Unique Ligands	AAC, CL
Unique branched monosaccharides	BGC, RER

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1RRV \| pdb_00001rrv	Download File View File

X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.

Mulichak, A.M., Lu, W., Losey, H.C., Walsh, C.T., Garavito, R.M.

(2004) Biochemistry 43: 5170

Released	2004-05-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Amycolatopsis orientalis
Macromolecule	DESVANCOSAMINYL VANCOMYCIN (protein) GLYCOSYLTRANSFERASE GTFD (protein)
Unique Ligands	BGC, GOL, K, TYD

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1SHO \| pdb_00001sho	Download File View File

CRYSTAL STRUCTURE OF VANCOMYCIN AT ATOMIC RESOLUTION

Sheldrick, G.M.

(1996) Structure 4: 1509

Released	1997-12-24
Method	X-RAY DIFFRACTION 1.09 Å
Organisms	Amycolatopsis orientalis
Macromolecule	VANCOMYCIN (protein)
Unique Ligands	ACT, CL
Unique branched monosaccharides	BGC, RER

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1TLP \| pdb_00001tlp	Download File View File

CRYSTALLOGRAPHIC STRUCTURAL ANALYSIS OF PHOSPHORAMIDATES AS INHIBITORS AND TRANSITION-STATE ANALOGS OF THERMOLYSIN

Tronrud, D.E., Monzingo, A.F., Matthews, B.W.

(1986) Eur J Biochem 157: 261-268

Released	1989-01-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus thermoproteolyticus
Macromolecule	THERMOLYSIN (protein)
Unique Ligands	CA, RDF, ZN

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2XAD \| pdb_00002xad	Download File View File

Crystal structure of deacetylase-teicoplanin complex in biosynthesis pathway of teicoplanin

Chan, H.C., Huang, Y.T., Lyu, S.Y., Huang, C.J., Li, Y.S., Liu, Y.C., Chou, C.C., Tsai, M.D., Li, T.L.

(2011) Mol Biosyst 7: 1224

Released	2011-03-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Actinoplanes teichomyceticus Nonomuraea gerenzanensis
Macromolecule	N-ACYL GLM PEUDO-TEICOPLANIN DEACETYLASE (protein) TEICOPLANIN (protein)
Unique Ligands	BMA, GCS, NAG, T55

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3DBK \| pdb_00003dbk	Download File View File

Pseudomonas aeruginosa elastase with phosphoramidon

McKay, D.B., Overgaard, M.T.

To be published

Released	2009-07-07
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Elastase (protein)
Unique Ligands	CA, RDF, SO4, ZN

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3DWB \| pdb_00003dwb	Download File View File

structure of human ECE-1 complexed with phosphoramidon

Oefner, C.

(2009) J Mol Biology 385: 178-187

Released	2008-11-25
Method	X-RAY DIFFRACTION 2.38 Å
Organisms	Homo sapiens
Macromolecule	Endothelin-converting enzyme 1 (protein)
Unique Ligands	5HD, RDF, ZN

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3RUN \| pdb_00003run	Download File View File

New strategy to analyze structures of glycopeptide antibiotic-target complexes

Economou, N.J., Townsend, T.M., Loll, P.J.

(2012) J Am Chem Soc 134: 4637-4645

Released	2012-06-06
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Amycolatopsis orientalis Tequatrovirus T4
Macromolecule	LYSOZYME (protein) VANCOMYCIN (protein)
Unique Ligands	CL, IPA, MPD, MRD, PO4, TRS
Unique branched monosaccharides	BGC, RER

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3VFJ \| pdb_00003vfj	Download File View File

The structure of monodechloro-teicoplanin in complex with its ligand, using MBP as a ligand carrier

Economou, N.J., Weeks, S.D., Grasty, K.C., Loll, P.J.

(2013) Acta Crystallogr D Biol Crystallogr 69: 520-533

Released	2013-01-09
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Actinoplanes teichomyceticus Escherichia coli K-12
Macromolecule	Maltose-binding periplasmic protein, C-terminal fused by Cys-Lys-D-Ala-D-Ala (protein) MonodeChloro- Teicoplanin A2-2 (protein)
Unique Ligands	ACT, CAC, GCS, MAN, NAG, T55, ZN

1 to 25 of 47 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1AA5 | pdb_00001aa5

1C0Q | pdb_00001c0q

1C0R | pdb_00001c0r

1DMT | pdb_00001dmt

1FVM | pdb_00001fvm

1GAC | pdb_00001gac

1GO6 | pdb_00001go6

1HH3 | pdb_00001hh3

1HHA | pdb_00001hha

1HHC | pdb_00001hhc

1HHF | pdb_00001hhf

1HHU | pdb_00001hhu

1HHY | pdb_00001hhy

1HHZ | pdb_00001hhz

1PN3 | pdb_00001pn3

1PNV | pdb_00001pnv

1QD8 | pdb_00001qd8

1RRV | pdb_00001rrv

1SHO | pdb_00001sho

1TLP | pdb_00001tlp

2XAD | pdb_00002xad

3DBK | pdb_00003dbk

3DWB | pdb_00003dwb

3RUN | pdb_00003run

3VFJ | pdb_00003vfj