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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 229 Structures.

Refinements

Structure Determination Methodology

experimental (229)

Scientific Name of Source Organism

	Escherichia coli (46)
	Homo sapiens (42)
	Saccharomyces cerevisiae (30)
	Escherichia coli K-12 (29)
	Oryctolagus cuniculus (11)
	Staphylococcus aureus subsp. aureus NCTC 8325 (10)
	Escherichia coli BL21 (7)
	Rattus norvegicus (7)
	Tetrahymena thermophila (6)
	synthetic construct (6)

More...

Taxonomy

	Eukaryota (122)
	Bacteria (110)
	other sequences (6)
	Archaea (5)
	Riboviria (4)
	unclassified sequences (1)

Experimental Method

	ELECTRON MICROSCOPY (139)
	X-RAY DIFFRACTION (90)

Polymer Entity Type

	Protein (217)
	RNA (149)
	DNA (4)
	NA-hybrid (1)

Refinement Resolution (Å)

	1.0 - 1.5 (9)
	1.5 - 2.0 (34)
	2.0 - 2.5 (61)
	2.5 - 3.0 (62)
	3.0 - 3.5 (44)
	3.5 - 4.0 (15)
	4.0 - 4.5 (2)
	> 4.5 (2)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (4)
	2000 - 2004 (1)
	2005 - 2009 (12)
	2010 - 2014 (14)
	2015 - 2019 (30)
	2020 - 2024 (161)
	2025 - 2029 (6)

Enzyme Classification Name

	Transferases (28)
	Hydrolases (27)
	Lyases (20)
	Oxidoreductases (7)
	Isomerases (7)
	Translocases (3)
	Ligases (1)

Membrane Protein Annotation

	PDBTM (13)
	MemProtMD (12)
	OPM (4)
	mpstruc (1)

Symmetry Type

	Asymmetric (175)
	Cyclic (33)
	Dihedral (10)

SCOP Classification

	Alpha and beta proteins (a/b) (15)
	Alpha and beta proteins (a+b) (6)
	All alpha proteins (2)
	Artifacts (1)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 229 Structures

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1BO4 \| pdb_00001bo4	Download File View File

CRYSTAL STRUCTURE OF A GCN5-RELATED N-ACETYLTRANSFERASE: SERRATIA MARESCENS AMINOGLYCOSIDE 3-N-ACETYLTRANSFERASE

Wolf, E., Vassilev, A., Makino, Y., Sali, A., Nakatani, Y., Burley, S.K.

(1998) Cell 94: 439-449

Released	1998-10-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Serratia marcescens
Macromolecule	PROTEIN (SERRATIA MARCESCENS AMINOGLYCOSIDE-3-N-ACETYLTRANSFERASE) (protein)
Unique Ligands	COA, SPD

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1I2X \| pdb_00001i2x	Download File View File

2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM

Tereshko, V., Wallace, S., Usman, N., Wincott, F., Egli, M.

(2001) RNA 7: 405-420

Released	2001-04-21
Method	X-RAY DIFFRACTION 2.4 Å
Macromolecule	DNA/RNA (5'-R(GPCPG)-D(PAPTPAPT)-R(PAPCPGP*U)-3') (hybrid)
Unique Ligands	SPD

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1POT \| pdb_00001pot	Download File View File

SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (MONOMER FORM)

Sugiyama, S., Maenaka, K., Matsushima, M., Morikawa, K.

(1996) Protein Sci 5: 1984-1990

Released	1996-12-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	SPERMIDINE/PUTRESCINE-BINDING PROTEIN (protein)
Unique Ligands	SPD

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1POY \| pdb_00001poy	Download File View File

SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)

Sugiyama, S., Vassylyev, D.G., Matsushima, M., Morikawa, K.

(1996) J Biological Chem 271: 9519-9525

Released	1996-07-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	SPERMIDINE/PUTRESCINE-BINDING PROTEIN (protein)
Unique Ligands	SPD

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1TYP \| pdb_00001typ	Download File View File

SUBSTRATE INTERACTIONS BETWEEN TRYPANOTHIONE REDUCTASE AND N1-GLUTATHIONYLSPERMIDINE DISULPHIDE AT 0.28-NM RESOLUTION

Bailey, S., Hunter, W.N.

(1993) Eur J Biochem 213: 67-75

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Crithidia fasciculata
Macromolecule	TRYPANOTHIONE REDUCTASE (protein)
Unique Ligands	FAD, GSH, NAP, SPD

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293D \| pdb_0000293d	Download File View File

INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE-2: THE CRYSTAL STRUCTURE OF THE D(CG)3 AND SPERMIDINE COMPLEX

Ohishi, H., Nakanishi, I., Inubushi, K., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Wang, A.H.-J., Hakoshima, T., Tomita, K.

(1996) FEBS Lett 391: 153-156

Released	1996-12-02
Method	X-RAY DIFFRACTION 1 Å
Macromolecule	DNA (5'-D(CPGPCPGPCPG)-3') (nucleic acid)
Unique Ligands	MG, NA, SPD

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2ELG \| pdb_00002elg	Download File View File

The rare crystallographic structure of d(CGCGCG)2: The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)2 at 10 degree celsius

Ohishi, H., Tozuka, Y., Zhou, D.Y., Ishida, T., Nakatani, K.

(2007) Biochem Biophys Res Commun 358: 24-28

Released	2008-04-01
Method	X-RAY DIFFRACTION 1 Å
Macromolecule	DNA (5'-D(DCPDGPDCPDGPDCPDG)-3') (nucleic acid)
Unique Ligands	MG, NA, SPD

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2HMP \| pdb_00002hmp	Download File View File

Uncomplexed actin cleaved with protease ECP32

Klenchin, V.A., Khaitlina, S.Y., Rayment, I.

(2006) J Mol Biology 362: 140-150

Released	2006-09-19
Method	X-RAY DIFFRACTION 1.899 Å
Organisms	Oryctolagus cuniculus
Macromolecule	actin, alpha skeletal muscle (protein)
Unique Ligands	211, ATP, EDO, SPD, SR

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2O07 \| pdb_00002o07	Download File View File

Human spermidine synthase

Min, J., Wu, H., Zeng, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

(2007) Biochemistry 46: 8331-8339

Released	2006-12-12
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Homo sapiens
Macromolecule	Spermidine synthase (protein)
Unique Ligands	MTA, SPD

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2P18 \| pdb_00002p18	Download File View File

Crystal structure of the Leishmania infantum glyoxalase II

Trincao, J., Barata, L., Najmudin, S., Bonifacio, C., Romao, M.J.

(2008) Biochemistry 47: 195-204

Released	2008-01-15
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Leishmania infantum
Macromolecule	Glyoxalase II (protein)
Unique Ligands	ACY, SPD, ZN

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2P1E \| pdb_00002p1e	Download File View File

Crystal structure of the Leishmania infantum glyoxalase II with D-Lactate at the active site

Trincao, J., Barata, L., Najmudin, S., Bonifacio, C., Romao, M.J.

(2008) Biochemistry 47: 195-204

Released	2008-01-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Leishmania infantum
Macromolecule	Glyoxalase II (protein)
Unique Ligands	LAC, SPD, ZN

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2PWP \| pdb_00002pwp	Download File View File

Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermidine

Qiu, W., Dong, A., Ren, H., Wu, H., Zhao, Y., Schapira, M., Wasney, G., Vedadi, M., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Plotnikov, A.N., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

To be published

Released	2007-05-22
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Plasmodium falciparum 3D7
Macromolecule	Spermidine synthase (protein)
Unique Ligands	GOL, SO4, SPD

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2QBY \| pdb_00002qby	Download File View File

Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)

Cunningham Dueber, E.L., Corn, J.E., Bell, S.D., Berger, J.M.

(2007) Science 317: 1210-1213

Released	2007-09-11
Method	X-RAY DIFFRACTION 3.35 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Cell division control protein 6 homolog 1 (protein) Cell division control protein 6 homolog 3 (protein) DNA (33-MER) (nucleic acid)
Unique Ligands	ADP, K, MG, SPD

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2YGP \| pdb_00002ygp	Download File View File

WIF domain-EGF-like domain 1 Met77Trp of human Wnt inhibitory factor 1 in complex with 1,2-dipalmitoylphosphatidylcholine

Malinauskas, T., Aricescu, A.R., Lu, W., Siebold, C., Jones, E.Y.

(2011) Nat Struct Mol Biol 18: 886

Released	2011-07-13
Method	X-RAY DIFFRACTION 2.222 Å
Organisms	Homo sapiens
Macromolecule	WNT INHIBITORY FACTOR 1 (protein)
Unique Ligands	CA, NAG, PCF, SPD

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3A76 \| pdb_00003a76	Download File View File

The crystal structure of LinA

Okai, M., Kubota, K., Fukuda, M., Nagata, Y., Nagata, K., Tanokura, M.

(2010) J Mol Biology

Released	2010-09-15
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Sphingomonas paucimobilis
Macromolecule	Gamma-hexachlorocyclohexane dehydrochlorinase (protein)
Unique Ligands	GOL, SPD

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3BXZ \| pdb_00003bxz	Download File View File

Crystal structure of the isolated DEAD motor domains from Escherichia coli SecA

Nithianantham, S., Namjoshi, S., Shilton, B.H.

(2008) J Mol Biology 383: 380-389

Released	2008-09-30
Method	X-RAY DIFFRACTION 3 Å
Organisms	Escherichia coli
Macromolecule	Preprotein translocase subunit secA (protein)
Unique Ligands	ADP, MG, SPD

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3C6K \| pdb_00003c6k	Download File View File

Crystal structure of human spermine synthase in complex with spermidine and 5-methylthioadenosine

Min, J., Wu, H., Zeng, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Pegg, A.E., Plotnikov, A.N., Structural Genomics Consortium (SGC)

(2008) J Biological Chem 283: 16135-16146

Released	2008-02-19
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	Spermine synthase (protein)
Unique Ligands	MTA, SPD

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3CN8 \| pdb_00003cn8	Download File View File

Crystal structure of fms1 in complex with spermidine

Huang, Q., Hao, Q.

To be published

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Polyamine oxidase FMS1 (protein)
Unique Ligands	FAD, SPD

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3GK7 \| pdb_00003gk7	Download File View File

Crystal structure of 4-hydroxybutyrate CoA-Transferase from Clostridium aminobutyricum

Messerschmidt, A., Macieira, S., Velarde, M.

(2009) Biol Chem 390: 1251-1263

Released	2009-12-22
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Clostridium aminobutyricum
Macromolecule	4-Hydroxybutyrate CoA-transferase (protein)
Unique Ligands	SPD, TRS

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3ICE \| pdb_00003ice	Download File View File

Rho transcription termination factor bound to RNA and ADP-BeF3

Thomsen, N.D., Berger, J.M.

(2009) Cell 139: 523-534

Released	2009-11-10
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli K-12
Macromolecule	Transcription termination factor rho (protein) 5'-R(PUPUPUPUPUPUPUPUPUPUPUPU)-3' (nucleic acid)
Unique Ligands	ADP, BEF, MG, SPD

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3L1R \| pdb_00003l1r	Download File View File

X-ray structure of the mutant lys300met of polyamine oxidase from zea mays in complex with spermidine

Fiorillo, A., Ilari, A., Tavladoraki, P.

To be published

Released	2010-12-15
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Zea mays
Macromolecule	Polyamine oxidase (protein)
Unique Ligands	CL, FAD, NAG, SO4, SPD
Unique branched monosaccharides	NAG

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3LS3 \| pdb_00003ls3	Download File View File

Padron0.9-ON (fluorescent state)

Brakemann, T., Weber, G., Trowitzsch, S., Wahl, M.C., Jakobs, S.

(2010) J Biological Chem 285: 14603-14609

Released	2010-03-16
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Pectiniidae
Macromolecule	Padron0.9 (protein)
Unique Ligands	EPE, GOL, SPD

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3LSA \| pdb_00003lsa	Download File View File

Padron0.9-OFF (non-fluorescent state)

Brakemann, T., Weber, G., Trowitzsch, S., Wahl, M.C., Jakobs, S.

(2010) J Biological Chem 285: 14603-14609

Released	2010-03-16
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Pectiniidae
Macromolecule	Padron0.9 (protein)
Unique Ligands	EPE, GOL, SO4, SPD

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3TTN \| pdb_00003ttn	Download File View File

Crystal structures of polyamine receptors SpuD and SpuE from Pseudomonas aeruginosa

Lim, S.C., Wu, D.H., Song, H.W.

(2012) J Mol Biology 416: 697-712

Released	2012-03-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Polyamine transport protein (protein)
Unique Ligands	SPD

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3WR7 \| pdb_00003wr7	Download File View File

Crystal Structure of Spermidine Acetyltransferase from Escherichia coli

Sugiyama, S., Ishikawa, S., Tomitori, S., Niiyama, M., Hirose, M., Miyazaki, Y., Higashi, K., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Kashiwagi, K., Igarashi, K., Matsumura, H.

(2016) Int J Biochem Cell Biol 76: 87-97

Released	2015-09-02
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli LY180
Macromolecule	Spermidine N1-acetyltransferase (protein)
Unique Ligands	COA, SPD

1 to 25 of 229 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

1BO4 | pdb_00001bo4

1I2X | pdb_00001i2x

1POT | pdb_00001pot

1POY | pdb_00001poy

1TYP | pdb_00001typ

293D | pdb_0000293d

2ELG | pdb_00002elg

2HMP | pdb_00002hmp

2O07 | pdb_00002o07

2P18 | pdb_00002p18

2P1E | pdb_00002p1e

2PWP | pdb_00002pwp

2QBY | pdb_00002qby

2YGP | pdb_00002ygp

3A76 | pdb_00003a76

3BXZ | pdb_00003bxz

3C6K | pdb_00003c6k

3CN8 | pdb_00003cn8

3GK7 | pdb_00003gk7

3ICE | pdb_00003ice

3L1R | pdb_00003l1r

3LS3 | pdb_00003ls3

3LSA | pdb_00003lsa

3TTN | pdb_00003ttn

3WR7 | pdb_00003wr7