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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yamamoto, K."

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Search Summary

This query matches 770 Structures.

Refinements

Structure Determination Methodology

experimental (770)

Scientific Name of Source Organism

	Homo sapiens (395)
	Severe acute respiratory syndrome coronavirus 2 (90)
	Mus musculus (53)
	synthetic construct (18)
	Rattus norvegicus (17)
	Bos taurus (15)
	Clostridium botulinum (14)
	Escherichia coli (13)
	Human immunodeficiency virus 1 (13)
	Lama glama (13)

More...

Taxonomy

	Eukaryota (527)
	Riboviria (186)
	Bacteria (173)
	other sequences (18)
	Eukaryota (eukaryotes) (11)
	unclassified sequences (8)
	Varidnaviria (6)
	Duplodnaviria (4)
	Archaea (2)
	Monodnaviria (2)

Experimental Method

	X-RAY DIFFRACTION (417)
	ELECTRON MICROSCOPY (333)
	SOLUTION NMR (18)
	ELECTRON CRYSTALLOGRAPHY (2)

Polymer Entity Type

	Protein (754)
	RNA (44)
	DNA (30)
	NA-hybrid (2)

Refinement Resolution (Å)

	1.0 - 1.5 (20)
	1.5 - 2.0 (100)
	2.0 - 2.5 (169)
	2.5 - 3.0 (196)
	3.0 - 3.5 (158)
	3.5 - 4.0 (65)
	4.0 - 4.5 (17)
	> 4.5 (27)

Release Date

	1990 - 1994 (3)
	1995 - 1999 (6)
	2000 - 2004 (3)
	2005 - 2009 (15)
	2010 - 2014 (64)
	2015 - 2019 (138)
	2020 - 2024 (515)
	2025 - 2029 (26)

Enzyme Classification Name

	Hydrolases (169)
	Transferases (77)
	Oxidoreductases (39)
	Translocases (10)
	Lyases (13)
	Ligases (7)
	Isomerases (4)

Membrane Protein Annotation

	PDBTM (110)
	mpstruc (78)
	OPM (70)
	MemProtMD (46)

Symmetry Type

	Asymmetric (501)
	Cyclic (194)
	Dihedral (23)
	Helical (18)
	Icosahedral (18)
	Octahedral (2)

SCOP Classification

	All beta proteins (51)
	Alpha and beta proteins (a+b) (50)
	Alpha and beta proteins (a/b) (34)
	All alpha proteins (27)
	Membrane and cell surface proteins and peptides (3)
	Artifacts (26)
	Small proteins (4)
	Peptides (2)

AllSelected

1 to 25 of 770 Structures

Page 1 of 31

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184D \| pdb_0000184d	Download File View File

SELF-ASSOCIATION OF A DNA LOOP CREATES A QUADRUPLEX: CRYSTAL STRUCTURE OF D(GCATGCT) AT 1.8 ANGSTROMS RESOLUTION

Leonard, G.A., Zhang, S., Peterson, M.R., Harrop, S.J., Helliwell, J.R., Cruse, W.B.T., Langlois D'Estaintot, B., Kennard, O., Brown, T., Hunter, W.N.

(1995) Structure 3: 335-340

Released	1995-07-10
Method	X-RAY DIFFRACTION 1.8 Å
Macromolecule	DNA (5'-D(GPCPAPTPGPCP*T)-3') (nucleic acid)
Unique Ligands	MG

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1BI0 \| pdb_00001bi0	Download File View File

STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR

Pohl, E., Hol, W.G.

(1998) J Biological Chem 273: 22420-22427

Released	1999-07-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Corynebacterium diphtheriae
Macromolecule	DIPHTHERIA TOXIN REPRESSOR (protein)
Unique Ligands	SO4, ZN

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1BI1 \| pdb_00001bi1	Download File View File

STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR

Pohl, E., Hol, W.G.J.

(1998) J Biological Chem 273: 22420-22427

Released	1999-06-22
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Corynebacterium diphtheriae
Macromolecule	DIPHTHERIA TOXIN REPRESSOR (protein)

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1BI2 \| pdb_00001bi2	Download File View File

STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR

Pohl, E., Hol, W.G.J.

(1998) J Biological Chem 273: 22420-22427

Released	1999-06-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Corynebacterium diphtheriae
Macromolecule	DIPHTHERIA TOXIN REPRESSOR (protein)

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1BI3 \| pdb_00001bi3	Download File View File

STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR

Pohl, E., Hol, W.G.J.

(1998) J Biological Chem 273: 22420-22427

Released	1999-06-22
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Corynebacterium diphtheriae
Macromolecule	DIPHTHERIA TOXIN REPRESSOR (protein)
Unique Ligands	SO4, ZN

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1D87 \| pdb_00001d87	Download File View File

CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL STRUCTURES OF DNA-RNA CHIMERIC DUPLEXES

Egli, M., Usman, N., Rich, A.

(1993) Biochemistry 32: 3221-3237

Released	1993-07-15
Method	X-RAY DIFFRACTION 2.25 Å
Macromolecule	DNA/RNA (5'-R(GP)-D(CPGPTPAPTPAPCPGP*C)-3') (hybrid)

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1D88 \| pdb_00001d88	Download File View File

CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL STRUCTURES OF DNA-RNA CHIMERIC DUPLEXES

Egli, M., Usman, N., Rich, A.

(1993) Biochemistry 32: 3221-3237

Released	1993-07-15
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	DNA/RNA (5'-D(GPCPGPTP)-R(AP)-D(TPAPCPGPC)-3') (hybrid)

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1G9I \| pdb_00001g9i	Download File View File

CRYSTAL STRUCTURE OF BETA-TRYSIN COMPLEX IN CYCLOHEXANE

Zhu, G., Huang, Q., Zhu, Y., Li, Y., Chi, C., Tang, Y.

(2001) Biochim Biophys Acta 1546: 98-106

Released	2000-12-06
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus Vigna radiata var. radiata
Macromolecule	BOWMAN-BIRK TYPE TRYPSIN INHIBITOR (protein) TRYPSINOGEN, CATIONIC (protein)
Unique Ligands	CA, SO4

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1HZ3 \| pdb_00001hz3	Download File View File

ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10-35)

Zhang, S., Iwata, K., Lachenmann, M.J., Peng, J.W., Li, S., Stimson, E.R., Lu, Y., Felix, A.M., Maggio, J.E., Lee, J.P.

(2000) J Struct Biol 130: 130-141

Released	2001-01-31
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	A-BETA AMYLOID (protein)

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1OZO \| pdb_00001ozo	Download File View File

Three-dimensional solution structure of apo-S100P protein determined by NMR spectroscopy

Lee, Y.-C., Volk, D.E., Thiviyanathan, V., Kleerekoper, Q., Gribenko, A.V., Zhang, S., Gorenstein, D.G., Makhatadze, G.I., Luxon, B.A.

(2004) J Biomol NMR 29: 399-402

Released	2004-04-20
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	S-100P protein (protein)

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1SMF \| pdb_00001smf	Download File View File

Studies on an artificial trypsin inhibitor peptide derived from the mung bean inhibitor

Huang, Q., Li, Y., Zhang, S., Liu, S., Tang, Y., Qi, C.

(1994) J Biochem 116: 18-25

Released	1994-07-31
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bos taurus Vigna radiata var. radiata
Macromolecule	BOWMAN-BIRK TYPE TRYPSIN INHIBITOR (protein) TRYPSIN (protein)
Unique Ligands	CA

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1VTH \| pdb_00001vth	Download File View File

DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURES OF D(TGTACA) COMPLEXED WITH DAUNOMYCIN

Nunn, C.M., Van Meervelt, L., Zhang, S., Moore, M.H., Kennard, O.

(1991) J Mol Biology 222: 167-177

Released	2011-07-13
Method	X-RAY DIFFRACTION 1.6 Å
Macromolecule	DNA (5'-D(TPGPTPAPCPA)-3') (nucleic acid)
Unique Ligands	DM1

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1VTI \| pdb_00001vti	Download File View File

DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURES OF D(TGATCA) COMPLEXED WITH DAUNOMYCIN

Nunn, C.M., Van Meervelt, L., Zhang, S., Moore, M.H., Kennard, O.

(1991) J Mol Biology 222: 167-177

Released	2011-07-13
Method	X-RAY DIFFRACTION 1.7 Å
Macromolecule	DNA (5'-D(TPGPTPAPCPA)-3') (nucleic acid)
Unique Ligands	DM1

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2F9Z \| pdb_00002f9z	Download File View File

Complex between the chemotaxis deamidase CheD and the chemotaxis phosphatase CheC from Thermotoga maritima

Chao, X., Park, S.Y., Bilwes, A.M., Crane, B.R.

(2006) Cell 124: 561-571

Released	2006-06-06
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermotoga maritima MSB8
Macromolecule	PROTEIN (chemotaxis methylation protein) (protein) chemotaxis protein CheC (protein)

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2G25 \| pdb_00002g25	Download File View File

E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin Diphosphate Complex

Furey, W., Arjunan, P., Chandrasekhar, K.

(2006) J Biological Chem 281: 15296-15303

Released	2006-04-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	Pyruvate dehydrogenase E1 component (protein)
Unique Ligands	MG, PO4, TDK

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2G28 \| pdb_00002g28	Download File View File

E. Coli Pyruvate Dehydrogenase H407A variant Phosphonolactylthiamin Diphosphate Complex

Furey, W., Arjunan, P., Chandrasekhar, K.

(2006) J Biological Chem 281: 15296-15303

Released	2006-04-25
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Escherichia coli
Macromolecule	Pyruvate dehydrogenase E1 component (protein)
Unique Ligands	MG, TDK

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2H8B \| pdb_00002h8b	Download File View File

Solution structure of INSL3

Rosengren, K.J., Craik, D.J., Daly, N.L.

(2006) J Biological Chem 281: 28287-28295

Released	2006-08-01
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Insulin-like 3 (protein)

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2K7X \| pdb_00002k7x	Download File View File

solution structure of C-terminal domain of SARS-CoV main protease

Xia, B., Zhong, N.

(2009) Protein Sci 18: 839-844

Released	2009-05-12
Method	SOLUTION NMR
Organisms	SARS coronavirus Sino1-11
Macromolecule	SARS-CoV main protease (protein)

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2KHP \| pdb_00002khp	Download File View File

Solution structure of Glutaredoxin from Brucella melitensis

Zheng, S., Leeper, T., Varani, G., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1141-1147

Released	2009-05-05
Method	SOLUTION NMR
Organisms	Brucella melitensis
Macromolecule	GLUTAREDOXIN (protein)

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2KLX \| pdb_00002klx	Download File View File

Solution structure of glutaredoxin from Bartonella henselae str. Houston

Leeper, T.C., Varani, G., Zheng, S., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1141-1147

Released	2009-07-28
Method	SOLUTION NMR
Organisms	Bartonella henselae str. Houston-1
Macromolecule	Glutaredoxin (protein)

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2LIZ \| pdb_00002liz	Download File View File

NMR solution structure of C-terminal domain of SARS-CoV main protease in 2.5M urea

Xia, B., Kang, X.

(2012) Proc Natl Acad Sci U S A 109: 14900-14905

Released	2012-09-05
Method	SOLUTION NMR
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-like proteinase (protein)

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2MDA \| pdb_00002mda	Download File View File

The Solution Structure of the Regulatory Domain of Tyrosine Hydroxylase

Zhang, S., Huang, T., Hinck, A., Fitzpatrick, P.

(2014) J Mol Biology 426: 1483-1497

Released	2014-01-01
Method	SOLUTION NMR
Organisms	Rattus norvegicus
Macromolecule	Tyrosine 3-monooxygenase (protein)

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2TDX \| pdb_00002tdx	Download File View File

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL

White, A., Ding, X., Zheng, H., Schiering, N., Ringe, D., Murphy, J.R.

(1998) Nature 394: 502-506

Released	1998-10-14
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Corynebacterium diphtheriae
Macromolecule	DIPHTHERIA TOX REPRESSOR (protein)
Unique Ligands	NI

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2XNI \| pdb_00002xni	Download File View File

Protein-ligand complex of a novel macrocyclic HCV NS3 protease inhibitor derived from amino cyclic boronates

Li, X., Zhang, Y.-K., Liu, Y., Ding, C.Z., Zhou, Y., Li, Q., Plattner, J.J., Baker, S.J., Zhang, S., Kazmierski, W.M., Wright, L.L., Smith, G.K., Grimes, R.M., Crosby, R.M., Creech, K.L., Carballo, L.H., Slater, M.J., Jarvest, R.L., Thommes, P., Hubbard, J.A., Convery, M.A., Nassau, P.M., McDowell, W., Skarzynski, T.J., Qian, X., Fan, D., Liao, L., Ni, Z.-J., Pennicott, L.E., Zou, W., Wright, J.

(2010) Bioorg Med Chem Lett 20: 5695

Released	2011-08-17
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Hepacivirus hominis
Macromolecule	NS3 PROTEASE (protein) NS4A COFACTOR (protein)
Unique Ligands	MG, TR8, ZN

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3CO3 \| pdb_00003co3	Download File View File

X-Ray Crystal Structure of a Monofunctional Platinum-DNA Adduct, cis-{Pt(NH3)2(pyridine)}2+ Bound to Deoxyguanosine in a Dodecamer Duplex

Lovejoy, K.S., Todd, R.C., Zhang, S., McCormick, M.S., D'Aquino, J.A., Reardon, J.T., Sancar, A., Giacomini, K.M., Lippard, S.J.

(2008) Proc Natl Acad Sci U S A 105: 8902-8907

Released	2008-06-10
Method	X-RAY DIFFRACTION 2.16 Å
Macromolecule	5'-D(DCPDCPDTPDCPDTPDCPDGPDTPDCPDTPDCPDC)-3' (nucleic acid) 5'-D(DGPDGPDAPDGPDAPDCPDGPDAPDGPDAPDGPDG)-3' (nucleic acid)
Unique Ligands	C7P

1 to 25 of 770 Structures

Page 1 of 31

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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

184D | pdb_0000184d

1BI0 | pdb_00001bi0

1BI1 | pdb_00001bi1

1BI2 | pdb_00001bi2

1BI3 | pdb_00001bi3

1D87 | pdb_00001d87

1D88 | pdb_00001d88

1G9I | pdb_00001g9i

1HZ3 | pdb_00001hz3

1OZO | pdb_00001ozo

1SMF | pdb_00001smf

1VTH | pdb_00001vth

1VTI | pdb_00001vti

2F9Z | pdb_00002f9z

2G25 | pdb_00002g25

2G28 | pdb_00002g28

2H8B | pdb_00002h8b

2K7X | pdb_00002k7x

2KHP | pdb_00002khp

2KLX | pdb_00002klx

2LIZ | pdb_00002liz

2MDA | pdb_00002mda

2TDX | pdb_00002tdx

2XNI | pdb_00002xni

3CO3 | pdb_00003co3