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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: BIRD Type = "Oligopeptide"

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Search Summary

This query matches 184 Structures.

Refinements

Structure Determination Methodology

experimental (184)

Scientific Name of Source Organism

	Homo sapiens (83)
	synthetic construct (41)
	Streptomyces argenteolus subsp. toyonakensis (19)
	Streptomyces roseus (14)
	Microcystis aeruginosa (12)
	Streptomyces (11)
	Escherichia coli K-12 (10)
	Escherichia coli (9)
	Hirudo medicinalis (9)
	Drosophila melanogaster (7)

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Taxonomy

	Eukaryota (130)
	Bacteria (108)
	other sequences (41)
	Riboviria (13)
	Duplodnaviria (1)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (165)
	ELECTRON MICROSCOPY (10)
	SOLUTION NMR (9)

Polymer Entity Type

	Protein (184)
	RNA (21)

Refinement Resolution (Å)

	0.5 - 1.0 (3)
	1.0 - 1.5 (17)
	1.5 - 2.0 (47)
	2.0 - 2.5 (53)
	2.5 - 3.0 (26)
	3.0 - 3.5 (14)
	3.5 - 4.0 (9)
	4.0 - 4.5 (2)
	> 4.5 (4)

Release Date

	1985 - 1989 (1)
	1990 - 1994 (6)
	1995 - 1999 (15)
	2000 - 2004 (19)
	2005 - 2009 (39)
	2010 - 2014 (51)
	2015 - 2019 (28)
	2020 - 2024 (25)

Enzyme Classification Name

	Hydrolases (115)
	Transferases (17)
	Ligases (5)
	Lyases (1)

Membrane Protein Annotation

	OPM (4)
	MemProtMD (3)
	PDBTM (3)
	mpstruc (1)

Symmetry Type

	Asymmetric (144)
	Cyclic (43)
	Dihedral (4)
	Helical (1)

SCOP Classification

	All beta proteins (41)
	Alpha and beta proteins (a+b) (27)
	Low resolution protein structures (1)
	All alpha proteins (8)
	Alpha and beta proteins (a/b) (11)
	Artifacts (6)
	Peptides (5)

AllSelected

1 to 25 of 184 Structures

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1A2C \| pdb_00001a2c	Download File View File

Structure of thrombin inhibited by AERUGINOSIN298-A from a BLUE-GREEN ALGA

Rios-Steiner, J.L., Murakami, M., Tulinsky, A.

(1998) J Am Chem Soc 120: 597

Released	1998-07-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Hirudo medicinalis Homo sapiens Microcystis aeruginosa
Macromolecule	Aeruginosin 298-A (protein) Hirudin variant-2 (protein) Thrombin heavy chain (protein) Thrombin light chain (protein)
Unique Ligands	NA

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1AJ1 \| pdb_00001aj1	Download File View File

NMR STRUCTURE OF THE LANTIBIOTIC ACTAGARDINE

Zimmermann, N., Jung, G.

(1997) Eur J Biochem 246: 809-819

Released	1997-10-15
Method	SOLUTION NMR
Organisms	Actinoplanes liguriensis
Macromolecule	LANTIBIOTIC ACTAGARDINE (protein)

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1APU \| pdb_00001apu	Download File View File

Crystallographic analysis of a pepstatin analogue binding to the aspartyl proteinase penicillopepsin at 1.8 angstroms resolution

Sielecki, A.R., James, M.N.G.

(1992) Biochemistry 31: 3872

Released	1994-01-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Penicillium janthinellum
Macromolecule	PEPSTATIN ANALOGUE ISOVALERYL-VAL-VAL-STA-O-ET (protein) PROTEIN (PENICILLOPEPSIN) (protein)
Unique Ligands	MAN

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1AQ7 \| pdb_00001aq7	Download File View File

TRYPSIN WITH INHIBITOR AERUGINOSIN 98-B

Sandler, B., Murakami, M., Clardy, J.

(1998) J Am Chem Soc 120: 595-596

Released	1998-02-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus Microcystis aeruginosa NIES-98
Macromolecule	AERUGINOSIN 98-B (protein) TRYPSIN (protein)

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1BCR \| pdb_00001bcr	Download File View File

COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, ANTIPAIN, AND ARGININE AT ROOM TEMPERATURE

Bullock, T.L., Remington, S.J.

(1996) J Mol Biology 255: 714-725

Released	1996-03-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Actinomycetes Triticum aestivum
Macromolecule	ANTIPAIN (protein) SERINE CARBOXYPEPTIDASE II (protein)
Unique Ligands	ARG, NAG
Unique branched monosaccharides	FUC, NAG

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1BCS \| pdb_00001bcs	Download File View File

COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, CHYMOSTATIN, AND ARGININE AT 100 DEGREES KELVIN

Bullock, T.L., Remington, S.J.

(1996) J Mol Biology 255: 714-725

Released	1996-03-08
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Streptomyces hygroscopicus Triticum aestivum
Macromolecule	CHYMOSTATIN A (protein) SERINE CARBOXYPEPTIDASE II (protein)
Unique Ligands	ACT, ARG, GOL, NAG
Unique branched monosaccharides	FUC, NAG, NDG

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1EVA \| pdb_00001eva	Download File View File

NMR structure of cyanobacterial toxin, phosphatase-1/-2A inhibitor

Bagu, J.R., Sykes, B.D.

(1995) Nat Struct Biol 2: 114-116

Released	1996-11-08
Method	SOLUTION NMR
Organisms	Microcystis
Macromolecule	MICROCYSTIN-LR (protein)

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1EVB \| pdb_00001evb	Download File View File

NMR structure of cyanobacterial toxin, phosphatase-1/-2A inhibitor

Bagu, J.R., Sykes, B.D.

(1995) Nat Struct Biol 2: 114-116

Released	1996-11-08
Method	SOLUTION NMR
Organisms	Microcystis
Macromolecule	MICROCYSTIN-LR (protein)

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1FJM \| pdb_00001fjm	Download File View File

Protein serine/threonine phosphatase-1 (alpha isoform, type 1) complexed with microcystin-LR toxin

Goldberg, J., Nairn, A.C., Kuriyan, J.

(1995) Nature 376: 745-753

Released	1996-06-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Microcystis aeruginosa Oryctolagus cuniculus
Macromolecule	PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1) (protein) microcystin LR (protein)
Unique Ligands	BME, MN

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1GHG \| pdb_00001ghg	Download File View File

CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON

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

(2001) J Med Chem 44: 1837

Released	2001-02-12
Method	X-RAY DIFFRACTION 0.98 Å
Organisms	Amycolatopsis orientalis
Macromolecule	VANCOMYCIN AGLYCON (protein)
Unique Ligands	ACY, DMS

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1H0I \| pdb_00001h0i	Download File View File

Complex of a chitinase with the natural product cyclopentapeptide argifin from Gliocladium

Houston, D.R., Shiomi, K., Arai, N., Omura, S., Peter, M.G., Turberg, A., Synstad, B., Eijsink, V.G.H., Aalten, D.M.F.

(2002) Proc Natl Acad Sci U S A 99: 9127

Released	2002-06-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Gliocladium Serratia marcescens
Macromolecule	ARGIFIN (protein) CHITINASE B (protein)
Unique Ligands	GOL, SO4

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1IZE \| pdb_00001ize	Download File View File

Crystal structure of Aspergillus oryzae Aspartic proteinase complexed with pepstatin

Kamitori, S., Ohtaki, A., Ino, H., Takeuchi, M.

(2003) J Mol Biology 326: 1503-1511

Released	2003-03-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Aspergillus oryzae Streptomyces argenteolus subsp. toyonakensis
Macromolecule	Pepstatin (protein) aspartic proteinase (protein)
Unique Ligands	MAN

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1J36 \| pdb_00001j36	Download File View File

Crystal Structure of Drosophila AnCE

Kim, H.M., Shin, D.R., Yoo, O.J., Lee, H., Lee, J.-O.

(2003) FEBS Lett 538: 65-70

Released	2003-07-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Drosophila melanogaster
Macromolecule	angiotensin converting enzyme (protein)
Unique Ligands	LPR, ZN

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1JRS \| pdb_00001jrs	Download File View File

HEMIACETAL COMPLEX BETWEEN LEUPEPTIN AND TRYPSIN

Kurinov, I.V., Harrison, R.W.

(1996) Protein Sci 5: 752-758

Released	1996-10-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus Streptomyces roseus
Macromolecule	Leupeptin (protein) TRYPSIN (protein)
Unique Ligands	CA

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1JRT \| pdb_00001jrt	Download File View File

HEMIACETAL COMPLEX BETWEEN LEUPEPTIN AND TRYPSIN

Kurinov, I.V., Harrison, R.W.

(1996) Protein Sci 5: 752-758

Released	1996-10-14
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Bos taurus
Macromolecule	LEUPEPTIN (protein) TRYPSIN (protein)
Unique Ligands	CA

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1LCM \| pdb_00001lcm	Download File View File

NMR minimized average structure of microcystin-LR

Trogen, G., Zdunek, J.

(1996) Biochemistry 35: 3197-3205

Released	1996-12-07
Method	SOLUTION NMR
Organisms	Microcystis aeruginosa
Macromolecule	microcystin LR (protein)

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1LS5 \| pdb_00001ls5	Download File View File

Crystal structure of plasmepsin IV from P. falciparum in complex with pepstatin A

Asojo, O.A., Gulnik, S.V., Afonina, E., Yu, B., Ellman, J.A., Haque, T.S., Silva, A.M.

(2003) J Mol Biology 327: 173-181

Released	2002-06-12
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Plasmodium falciparum Streptomyces argenteolus subsp. toyonakensis
Macromolecule	Pepstatin (protein) plasmepsin IV (protein)

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1LYB \| pdb_00001lyb	Download File View File

CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN

Baldwin, E.T., Bhat, T.N., Gulnik, S., Erickson, J.W.

(1993) Proc Natl Acad Sci U S A 90: 6796-6800

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens Streptomyces argenteolus subsp. toyonakensis
Macromolecule	CATHEPSIN D (protein) PEPSTATIN (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, MAN, NAG

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1M21 \| pdb_00001m21	Download File View File

Crystal structure analysis of the peptide amidase PAM in complex with the competitive inhibitor chymostatin

Labahn, J., Neumann, S., Buldt, G., Kula, M.-R., Granzin, J.

(2002) J Mol Biology 322: 1053-1064

Released	2002-10-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Stenotrophomonas maltophilia Streptomyces hygroscopicus
Macromolecule	CHYMOSTATIN (protein) Peptide Amidase (protein)

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1M43 \| pdb_00001m43	Download File View File

Crystal structure of PMII in complex with pepstatin a to 2.4 A

Asojo, O.A., Silva, A.M., Gulnik, S.

To be published

Released	2002-07-24
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Plasmodium falciparum Streptomyces argenteolus subsp. toyonakensis
Macromolecule	Pepstatin (protein) plasmepsin II (protein)

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1MQX \| pdb_00001mqx	Download File View File

NMR Solution Structure of Type-B Lantibiotics Mersacidin in MeOH/H2O Mixture

Hsu, S.-T., Breukink, E., Bierbaum, G., Sahl, H.-G., de Kruijff, B., Kaptein, R., van Nuland, N.A., Bonvin, A.M.

(2003) J Biological Chem 278: 13110

Released	2003-03-11
Method	SOLUTION NMR
Organisms	Bacillus sp. HIL-Y85/54728
Macromolecule	LANTIBIOTIC MERSACIDIN (protein)

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1MQY \| pdb_00001mqy	Download File View File

NMR solution structure of type-B lantibiotics mersacidin in DPC micelles

Hsu, S.-T., Breukink, E., Bierbaum, G., Sahl, H.-G., de Kruijff, B., Kaptein, R., van Nuland, N.A., Bonvin, A.M.

(2003) J Biological Chem 278: 13110

Released	2003-03-11
Method	SOLUTION NMR
Organisms	Bacillus sp. HIL-Y85/54728
Macromolecule	LANTIBIOTIC MERSACIDIN (protein)

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1MQZ \| pdb_00001mqz	Download File View File

NMR solution structure of type-B lantibiotics mersacidin bound to lipid II in DPC micelles

Hsu, S.-T., Breukink, E., Bierbaum, G., Sahl, H.-G., de Kruijff, B., Kaptein, R., van Nuland, N.A., Bonvin, A.M.

(2003) J Biological Chem 278: 13110

Released	2003-03-11
Method	SOLUTION NMR
Organisms	Bacillus sp. HIL-Y85/54728
Macromolecule	LANTIBIOTIC MERSACIDIN (protein)

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1NZQ \| pdb_00001nzq	Download File View File

D-Phe-Pro-Arg-Type Thrombin Inhibitor

Lange, U.E., Bauke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

(2003) Bioorg Med Chem Lett 13: 2029-2033

Released	2003-10-14
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Homo sapiens
Macromolecule	Decapeptide Hirudin Analogue (protein) Thrombin heavy chain (protein) Thrombin light chain (protein)
Unique Ligands	162

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1O0D \| pdb_00001o0d	Download File View File

Human Thrombin complexed with a d-Phe-Pro-Arg-type Inhibitor and a C-terminal Hirudin derived exo-site inhibitor

Lange, U.E., Bauke, D., Hornberger, W., Mack, H., Seitz, W., Hoeffken, H.W.

(2003) Bioorg Med Chem Lett 13: 2029-2033

Released	2003-10-14
Method	X-RAY DIFFRACTION 2.44 Å
Organisms	Homo sapiens
Macromolecule	Decapeptide Hirudin Analogue (protein) Thrombin heavy chain (protein) Thrombin light chain (protein)
Unique Ligands	163

1 to 25 of 184 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

1A2C | pdb_00001a2c

1AJ1 | pdb_00001aj1

1APU | pdb_00001apu

1AQ7 | pdb_00001aq7

1BCR | pdb_00001bcr

1BCS | pdb_00001bcs

1EVA | pdb_00001eva

1EVB | pdb_00001evb

1FJM | pdb_00001fjm

1GHG | pdb_00001ghg

1H0I | pdb_00001h0i

1IZE | pdb_00001ize

1J36 | pdb_00001j36

1JRS | pdb_00001jrs

1JRT | pdb_00001jrt

1LCM | pdb_00001lcm

1LS5 | pdb_00001ls5

1LYB | pdb_00001lyb

1M21 | pdb_00001m21

1M43 | pdb_00001m43

1MQX | pdb_00001mqx

1MQY | pdb_00001mqy

1MQZ | pdb_00001mqz

1NZQ | pdb_00001nzq

1O0D | pdb_00001o0d