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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Matsui, Y."

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Search Summary

This query matches 257 Structures.

Refinements

Structure Determination Methodology

experimental (257)

Scientific Name of Source Organism

	Homo sapiens (35)
	Cystovirus phi6 (28)
	Influenza A virus (A/Brevig Mission/1/1918(H1N1)) (23)
	synthetic construct (23)
	Camelidae mixed library (18)
	human metapneumovirus (17)
	Pseudomonas phage phi12 (16)
	Staphylococcus aureus (14)
	Influenza C virus (C/Johannesburg/1/66) (9)
	dengue virus type 2 (9)

More...

Taxonomy

	Riboviria (185)
	Eukaryota (81)
	Bacteria (32)
	other sequences (23)
	Varidnaviria (22)
	Viruses incertae sedis (4)
	Monodnaviria (3)

Experimental Method

	X-RAY DIFFRACTION (203)
	ELECTRON MICROSCOPY (54)

Polymer Entity Type

	Protein (256)
	RNA (45)
	DNA (12)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (36)
	2.0 - 2.5 (53)
	2.5 - 3.0 (56)
	3.0 - 3.5 (57)
	3.5 - 4.0 (15)
	4.0 - 4.5 (14)
	> 4.5 (21)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (4)
	2000 - 2004 (22)
	2005 - 2009 (43)
	2010 - 2014 (50)
	2015 - 2019 (63)
	2020 - 2024 (72)
	2025 - 2029 (2)

Enzyme Classification Name

	Transferases (100)
	Hydrolases (60)
	Lyases (4)
	Isomerases (1)
	Oxidoreductases (1)

Membrane Protein Annotation

	OPM (8)
	MemProtMD (5)
	PDBTM (6)
	mpstruc (6)

Symmetry Type

	Asymmetric (169)
	Cyclic (76)
	Icosahedral (9)
	Dihedral (5)

SCOP Classification

	All beta proteins (22)
	Alpha and beta proteins (a/b) (29)
	Multi-domain proteins (alpha and beta) (21)
	Artifacts (12)
	Low resolution protein structures (1)
	All alpha proteins (1)
	Alpha and beta proteins (a+b) (5)
	Membrane and cell surface proteins and peptides (3)
	Small proteins (2)
	Peptides (1)

AllSelected

1 to 25 of 257 Structures

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1ALD \| pdb_00001ald	Download File View File

ACTIVITY AND SPECIFICITY OF HUMAN ALDOLASES

Watson, H.C.

(1991) J Mol Biology 219: 573-576

Released	1992-01-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	ALDOLASE A (protein)

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1D4V \| pdb_00001d4v	Download File View File

Crystal structure of trail-DR5 complex

Mongkolsapaya, J., Grimes, J.M., Stuart, D.I., Jones, E.Y., Screaton, G.R.

(1999) Nat Struct Biol 6: 1048-1053

Released	1999-11-01
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DEATH RECEPTOR 5 (protein) TNF-RELATED APOPTOSIS INDUCING LIGAND (protein)

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1H1K \| pdb_00001h1k	Download File View File

THE BLUETONGUE VIRUS (BTV) CORE BINDS DSRNA

Diprose, J.M., Grimes, J.M., Sutton, G.C., Burroughs, J.N., Meyer, A., Maan, S., Mertens, P.P.C., Stuart, D.I.

(2002) J Virol 76: 9533

Released	2002-09-26
Method	X-RAY DIFFRACTION 10 Å
Organisms	Bluetongue virus
Macromolecule	Unique nucleic acid chains: 6

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1HHS \| pdb_00001hhs	Download File View File

RNA dependent RNA polymerase from dsRNA bacteriophage phi6

Grimes, J.M., Butcher, S.J., Makeyev, E.V., Bamford, D.H., Stuart, D.I.

(2001) Nature 410: 235

Released	2001-03-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Cystovirus phi6
Macromolecule	RNA-DIRECTED RNA POLYMERASE (protein)
Unique Ligands	MN

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1HHT \| pdb_00001hht	Download File View File

RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus template

Grimes, J.M., Butcher, S.J., Makeyev, E.V., Bamford, D.H., Stuart, D.I.

(2001) Nature 410: 235

Released	2001-03-27
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Cystovirus phi6
Macromolecule	P2 PROTEIN (protein) DNA (5'-(TPTPTPCP*C)-3') (nucleic acid)
Unique Ligands	MN

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1HI0 \| pdb_00001hi0	Download File View File

RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus initiation complex

Grimes, J.M., Butcher, S.J., Makeyev, E.V., Bamford, D.H., Stuart, D.I.

(2001) Nature 410: 235

Released	2001-03-27
Method	X-RAY DIFFRACTION 3 Å
Organisms	Cystovirus phi6
Macromolecule	P2 PROTEIN (protein) DNA (5'-(TPTPTPCP*C)-3') (nucleic acid)
Unique Ligands	GTP, MG, MN

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1HI1 \| pdb_00001hi1	Download File View File

RNA dependent RNA polymerase from dsRNA bacteriophage phi6 plus bound NTP

Grimes, J.M., Butcher, S.J., Makeyev, E.V., Bamford, D.H., Stuart, D.I.

(2001) Nature 410: 235

Released	2001-03-27
Method	X-RAY DIFFRACTION 3 Å
Organisms	Cystovirus phi6
Macromolecule	P2 PROTEIN (protein)
Unique Ligands	ATP

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1HI8 \| pdb_00001hi8	Download File View File

RNA dependent RNA polymerase from dsRNA bacteriophage phi6

Grimes, J.M., Butcher, S.J., Makeyev, E.V., Bamford, D.H., Stuart, D.I.

(2001) Nature 410: 235

Released	2001-03-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Cystovirus phi6
Macromolecule	P2 PROTEIN (protein)
Unique Ligands	MG

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1UVI \| pdb_00001uvi	Download File View File

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 6nt RNA

Salgado, P.S., Makeyev, E.V., Butcher, S., Bamford, D., Stuart, D.I., Grimes, J.M.

(2004) Structure 12: 307-316

Released	2004-02-19
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Cystovirus phi6 synthetic construct
Macromolecule	RNA-directed RNA polymerase (protein) 5'-R(UPUPUPUPCPCP)-3' (nucleic acid)
Unique Ligands	MN

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1UVJ \| pdb_00001uvj	Download File View File

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 7nt RNA

Salgado, P.S., Makeyev, E.V., Butcher, S., Bamford, D., Stuart, D.I., Grimes, J.M.

(2004) Structure 12: 307-316

Released	2004-02-19
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Cystovirus phi6 synthetic construct
Macromolecule	RNA-directed RNA polymerase (protein) 5'-R(UPUPCPCP)-3' (nucleic acid)
Unique Ligands	MN

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1UVK \| pdb_00001uvk	Download File View File

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complex

Salgado, P.S., Makeyev, E.V., Butcher, S., Bamford, D., Stuart, D.I., Grimes, J.M.

(2004) Structure 12: 307-316

Released	2004-02-19
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Cystovirus phi6
Macromolecule	RNA-directed RNA polymerase (protein)
Unique Ligands	G, GTP, MG, MN, POP

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1UVL \| pdb_00001uvl	Download File View File

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 5nt RNA. Conformation B

Salgado, P.S., Makeyev, E.V., Butcher, S., Bamford, D., Stuart, D.I., Grimes, J.M.

(2004) Structure 12: 307-316

Released	2004-02-26
Method	X-RAY DIFFRACTION 2 Å
Organisms	Cystovirus phi6 synthetic construct
Macromolecule	RNA-directed RNA polymerase (protein) 5'-R(UPUPUPCP*CP)-3' (nucleic acid)
Unique Ligands	MN

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1UVM \| pdb_00001uvm	Download File View File

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 5NT RNA conformation A

Salgado, P.S., Makeyev, E.V., Butcher, S., Bamford, D., Stuart, D.I., Grimes, J.M.

(2004) Structure 12: 307-316

Released	2004-02-19
Method	X-RAY DIFFRACTION 2 Å
Organisms	Cystovirus phi6 synthetic construct
Macromolecule	RNA-directed RNA polymerase (protein) 5'-R(UPUPUPCP*CP)-3' (nucleic acid)
Unique Ligands	MN

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1UVN \| pdb_00001uvn	Download File View File

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 ca2+ inhibition complex

Salgado, P.S., Makeyev, E.V., Butcher, S., Bamford, D., Stuart, D.I., Grimes, J.M.

(2004) Structure 12: 307-316

Released	2004-02-26
Method	X-RAY DIFFRACTION 3 Å
Organisms	Cystovirus phi6 synthetic construct
Macromolecule	RNA-directed RNA polymerase (protein) 5'-R(UPUPUPUPCPCP)-3' (nucleic acid)
Unique Ligands	CA, GTP, MN

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1UW7 \| pdb_00001uw7	Download File View File

Nsp9 protein from SARS-coronavirus.

Sutton, G., Fry, E., Carter, L., Sainsbury, S., Walter, T., Nettleship, J., Berrow, N., Owens, R., Gilbert, R., Davidson, A., Siddell, S., Poon, L.L.M., Diprose, J., Alderton, D., Walsh, M., Grimes, J.M., Stuart, D.I.

(2004) Structure 12: 341

Released	2004-02-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	SARS coronavirus HKU-39849
Macromolecule	NSP9 (protein)

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1UZK \| pdb_00001uzk	Download File View File

Integrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-1, Ca bound to cbEGF23 domain only

Lee, S.S.J., Knott, V., Harlos, K., Handford, P.A., Stuart, D.I.

(2004) Structure 12: 717

Released	2006-05-24
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Homo sapiens
Macromolecule	FIBRILLIN-1 (protein)
Unique Ligands	CA

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1W44 \| pdb_00001w44	Download File View File

P4 protein from Bacteriophage PHI12 in complex with ADP

Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I.

(2004) Cell 118: 743

Released	2004-10-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas phage phi12
Macromolecule	NTPASE P4 (protein)
Unique Ligands	ADP

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1W46 \| pdb_00001w46	Download File View File

P4 protein from Bacteriophage PHI12 in complex with ADP and MG

Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I.

(2004) Cell 118: 743

Released	2004-11-04
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Pseudomonas phage phi12
Macromolecule	NTPASE P4 (protein)
Unique Ligands	ADP, MG

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1W47 \| pdb_00001w47	Download File View File

P4 protein from Bacteriophage PHI12 in complex with ADP and MN

Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I.

(2004) Cell 118: 743

Released	2004-11-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pseudomonas phage phi12
Macromolecule	NTPASE P4 (protein)
Unique Ligands	ADP, MN

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1W48 \| pdb_00001w48	Download File View File

P4 protein from Bacteriophage PHI12 in complex with AMPcPP

Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I.

(2004) Cell 118: 743

Released	2004-10-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pseudomonas phage phi12
Macromolecule	NTPASE P4 (protein)
Unique Ligands	APC

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1W49 \| pdb_00001w49	Download File View File

P4 protein from Bacteriophage PHI12 in complex with AMPcPP and Mg

Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I.

(2004) Cell 118: 743

Released	2004-10-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Pseudomonas phage phi12
Macromolecule	NTPASE P4 (protein)
Unique Ligands	APC, MG

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1W4A \| pdb_00001w4a	Download File View File

P4 protein from PHI12 in complex with AMPcPP and Mn

Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I.

(2004) Cell 118: 743

Released	2004-10-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Pseudomonas phage phi12
Macromolecule	NTPASE P4 (protein)
Unique Ligands	APC, MN

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1W4B \| pdb_00001w4b	Download File View File

P4 protein from PHI12 in complex with product (AMPcPP Mg 22C)

Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I.

(2004) Cell 118: 743

Released	2004-11-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pseudomonas phage phi12
Macromolecule	NTPASE P4 (protein)
Unique Ligands	ADP, MG

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1W4C \| pdb_00001w4c	Download File View File

P4 protein from Bacteriophage PHI12 apo state

Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I.

(2004) Cell 118: 743

Released	2004-11-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pseudomonas phage phi12
Macromolecule	NTPASE P4 (protein)

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1W8X \| pdb_00001w8x	Download File View File

Structural analysis of PRD1

Abrescia, N.G.A., Cockburn, J.J.B., Grimes, J.M., Sutton, G.C., Diprose, J.M., Butcher, S.J., Fuller, S.D., San Martin, C., Burnett, R.M., Stuart, D.I., Bamford, D.H., Bamford, J.K.H.

(2004) Nature 432: 68

Released	2004-11-11
Method	X-RAY DIFFRACTION 4.2 Å
Organisms	Enterobacteria phage PRD1
Macromolecule	MAJOR CAPSID PROTEIN (PROTEIN P3) (protein) PROTEIN P16 (protein) PROTEIN P30 (protein) PROTEIN P31 (protein)

1 to 25 of 257 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

1ALD | pdb_00001ald

1D4V | pdb_00001d4v

1H1K | pdb_00001h1k

1HHS | pdb_00001hhs

1HHT | pdb_00001hht

1HI0 | pdb_00001hi0

1HI1 | pdb_00001hi1

1HI8 | pdb_00001hi8

1UVI | pdb_00001uvi

1UVJ | pdb_00001uvj

1UVK | pdb_00001uvk

1UVL | pdb_00001uvl

1UVM | pdb_00001uvm

1UVN | pdb_00001uvn

1UW7 | pdb_00001uw7

1UZK | pdb_00001uzk

1W44 | pdb_00001w44

1W46 | pdb_00001w46

1W47 | pdb_00001w47

1W48 | pdb_00001w48

1W49 | pdb_00001w49

1W4A | pdb_00001w4a

1W4B | pdb_00001w4b

1W4C | pdb_00001w4c

1W8X | pdb_00001w8x