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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Shoham, Y."

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Search Summary

This query matches 74 Structures.

Refinements

Structure Determination Methodology

experimental (74)

Scientific Name of Source Organism

	Homo sapiens (42)
	Neisseria meningitidis (8)
	Neisseria meningitidis serogroup B (5)
	Human alphaherpesvirus 3 (4)
	Mus musculus (4)
	Neisseria meningitidis MC58 (4)
	Human respiratory syncytial virus A2 (3)
	Severe acute respiratory syndrome coronavirus 2 (3)
	Staphylococcus aureus subsp. aureus NCTC 8325 (3)
	Staphylococcus pseudintermedius (3)

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Taxonomy

	Eukaryota (47)
	Bacteria (32)
	Riboviria (9)
	Duplodnaviria (8)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (62)
	ELECTRON MICROSCOPY (6)
	SOLUTION NMR (6)

Polymer Entity Type

	Protein (74)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (19)
	2.0 - 2.5 (17)
	2.5 - 3.0 (15)
	3.0 - 3.5 (9)
	3.5 - 4.0 (3)
	4.0 - 4.5 (3)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (4)
	2005 - 2009 (15)
	2010 - 2014 (17)
	2015 - 2019 (15)
	2020 - 2024 (22)

Enzyme Classification Name

	Hydrolases (16)
	Transferases (4)
	Isomerases (1)

Symmetry Type

	Asymmetric (58)
	Cyclic (18)

SCOP Classification

	All beta proteins (16)
	Alpha and beta proteins (a/b) (10)
	Artifacts (9)
	Alpha and beta proteins (a+b) (5)
	Small proteins (7)
	Membrane and cell surface proteins and peptides (2)
	All alpha proteins (1)

AllSelected

1 to 25 of 74 Structures

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1D8B \| pdb_00001d8b	Download File View File

NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE

Liu, Z., Macias, M.J., Bottomley, M.J., Stier, G., Linge, J.P., Nilges, M., Bork, P., Sattler, M.

(1999) Structure 7: 1557-1566

Released	2000-01-10
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	SGS1 RECQ HELICASE (protein)

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1H5P \| pdb_00001h5p	Download File View File

Solution structure of the human Sp100b SAND domain by heteronuclear NMR.

Bottomley, M.J., Liu, Z., Collard, M.W., Huggenvik, J.I., Gibson, T.J., Sattler, M.

(2001) Nat Struct Biol 8: 626-633

Released	2001-07-06
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	NUCLEAR AUTOANTIGEN SP100-B (protein)

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1K1G \| pdb_00001k1g	Download File View File

STRUCTURAL BASIS FOR RECOGNITION OF THE INTRON BRANCH SITE RNA BY SPLICING FACTOR 1

Liu, Z., Luyten, I., Bottomley, M.J., Messias, A.C., Houngninou-Molango, S., Sprangers, R., Zanier, K., Kramer, A., Sattler, M.

(2001) Science 294: 1098-1102

Released	2001-11-07
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	SF1-Bo isoform (protein) 5'-R(UPAPUPAPCPUPAPAPCPAP*A)-3' (nucleic acid)

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1OQJ \| pdb_00001oqj	Download File View File

Crystal structure of the SAND domain from glucocorticoid modulatory element binding protein-1 (GMEB1)

Surdo, P.L., Bottomley, M.J., Sattler, M., Scheffzek, K.

(2003) Mol Endocrinol 17: 1283-1295

Released	2003-11-11
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Glucocorticoid Modulatory Element Binding protein-1 (protein)
Unique Ligands	ZN

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1VCA \| pdb_00001vca	Download File View File

CRYSTAL STRUCTURE OF AN INTEGRIN-BINDING FRAGMENT OF VASCULAR CELL ADHESION MOLECULE-1 AT 1.8 ANGSTROMS RESOLUTION

Jones, E.Y., Harlos, K., Bottomley, M.J., Robinson, R.C., Driscoll, P.C., Edwards, R.M., Clements, J.M., Dudgeon, T.J., Stuart, D.I.

(1995) Nature 373: 539-544

Released	1995-09-15
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	HUMAN VASCULAR CELL ADHESION MOLECULE-1 (protein)

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1XWH \| pdb_00001xwh	Download File View File

NMR structure of the first phd finger of autoimmune regulator protein (AIRE1): insights into apeced

Bottomley, M.J., Stier, G., Krasotkina, J., Legube, G., Simon, B., Akhtar, A., Sattler, M., Musco, G.

(2005) J Biological Chem 280: 11505-11512

Released	2005-01-25
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Autoimmune regulator (protein)
Unique Ligands	ZN

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2JW6 \| pdb_00002jw6	Download File View File

Solution structure of the DEAF1 MYND domain

Spadaccini, R., Perrin, H., Bottomley, M., Ansieu, S., Sattler, M.

(2008) J Mol Biology 376: 1523-1523

Released	2007-12-25
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Deformed epidermal autoregulatory factor 1 homolog (protein)
Unique Ligands	ZN

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2K1Q \| pdb_00002k1q	Download File View File

NMR structure of hepatitis c virus ns3 serine protease complexed with the non-covalently bound phenethylamide inhibitor

Eliseo, T., Gallo, M., Pennestri, M., Bazzo, R., Cicero, D.O.

(2009) J Mol Biology 385: 1142-1155

Released	2009-02-03
Method	SOLUTION NMR
Organisms	Hepacivirus hominis
Macromolecule	NS3 PROTEASE (protein) PHENETHYLAMIDE (protein)
Unique Ligands	ZN

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2UV0 \| pdb_00002uv0	Download File View File

Structure of the P. aeruginosa LasR ligand-binding domain bound to its autoinducer

Bottomley, M.J., Muraglia, E., Bazzo, R., Carfi, A.

(2007) J Biological Chem 282: 13592

Released	2007-03-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR (protein)
Unique Ligands	OHN

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2VQJ \| pdb_00002vqj	Download File View File

Structure of HDAC4 catalytic domain bound to a trifluoromethylketone inhbitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-08
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	DIO, K, SO4, TFG, ZN

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2VQM \| pdb_00002vqm	Download File View File

Structure of HDAC4 catalytic domain bound to a hydroxamic acid inhbitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	HA3, K, ZN

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2VQO \| pdb_00002vqo	Download File View File

Structure of HDAC4 catalytic domain with a gain-of-function muation bound to a trifluoromethylketone inhbitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-08
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	K, SO4, TFG, ZN

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2VQQ \| pdb_00002vqq	Download File View File

Structure of HDAC4 catalytic domain (a double cysteine-to-alanine mutant) bound to a trifluoromethylketone inhbitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-08
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	K, SO4, TFG, ZN

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2VQV \| pdb_00002vqv	Download File View File

Structure of HDAC4 catalytic domain with a gain-of-function mutation bound to a hydroxamic acid inhibitor

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-07-22
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	HA3, K, SO4, ZN

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2VQW \| pdb_00002vqw	Download File View File

Structure of inhibitor-free HDAC4 catalytic domain (with gain-of- function mutation His332Tyr)

Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

(2008) J Biological Chem 283: 26694

Released	2008-08-05
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	HISTONE DEACETYLASE 4 (protein)
Unique Ligands	K, ZN

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2W2M \| pdb_00002w2m	Download File View File

WT PCSK9-DELTAC BOUND TO WT EGF-A OF LDLR

Bottomley, M.J., Cirillo, A., Orsatti, L., Ruggeri, L., Fisher, T.S., Santoro, J.C., Cummings, R.T., Cubbon, R.M., Lo Surdo, P., Calzetta, A., Noto, A., Baysarowich, J., Mattu, M., Talamo, F., De Francesco, R., Sparrow, C.P., Sitlani, A., Carfi, A.

(2009) J Biological Chem 284: 1313

Released	2008-11-18
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	LOW-DENSITY LIPOPROTEIN RECEPTOR (protein) PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 (protein)
Unique Ligands	CA

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2W2N \| pdb_00002w2n	Download File View File

WT PCSK9-deltaC bound to EGF-A H306Y mutant of LDLR

(2009) J Biological Chem 284: 1313

Released	2008-11-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	LOW-DENSITY LIPOPROTEIN RECEPTOR (protein) PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 (protein)
Unique Ligands	CA

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2W2O \| pdb_00002w2o	Download File View File

PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR

(2009) J Biological Chem 284: 1313

Released	2008-11-18
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Homo sapiens
Macromolecule	LOW-DENSITY LIPOPROTEIN RECEPTOR (protein) PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 (protein)
Unique Ligands	CA

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2W2P \| pdb_00002w2p	Download File View File

PCSK9-deltaC D374A mutant bound to WT EGF-A of LDLR

(2009) J Biological Chem 284: 1313

Released	2008-11-18
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Homo sapiens
Macromolecule	LOW-DENSITY LIPOPROTEIN RECEPTOR (protein) PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 (protein)
Unique Ligands	CA

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2W2Q \| pdb_00002w2q	Download File View File

PCSK9-deltaC D374H mutant bound to WT EGF-A of LDLR

(2009) J Biological Chem 284: 1313

Released	2008-11-18
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Homo sapiens
Macromolecule	LOW-DENSITY LIPOPROTEIN RECEPTOR (protein) PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 (protein)
Unique Ligands	CA

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2XTJ \| pdb_00002xtj	Download File View File

The crystal structure of PCSK9 in complex with 1D05 Fab

Di Marco, S., Volpari, C., Carfi, A.

(2011) J Lipid Res 52: 78

Released	2010-11-03
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6
Unique Ligands	CA

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2Y7S \| pdb_00002y7s	Download File View File

Structure of a designed meningococcal antigen (factor H binding protein, mutant G1) inducing broad protective immunity

Malito, E., Spraggon, G., Bottomley, M.J.

(2011) Sci Transl Med 3: 91RA6

Released	2011-07-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Neisseria meningitidis MC58
Macromolecule	FACTOR H BINDING PROTEIN (protein)

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2YPV \| pdb_00002ypv	Download File View File

Crystal structure of the Meningococcal vaccine antigen factor H binding protein in complex with a bactericidal antibody

Malito, E., Veggi, D., Bottomley, M.J.

(2013) Proc Natl Acad Sci U S A 110: 3304

Released	2013-02-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mus musculus Neisseria meningitidis MC58
Macromolecule	FAB 12C1 (protein) LIPOPROTEIN (protein)
Unique Ligands	EDO

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3P5B \| pdb_00003p5b	Download File View File

The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation

Lo Surdo, P., Bottomley, M.J., Calzetta, A., Settembre, E.C., Cirillo, A., Pandit, S., Ni, Y., Hubbard, B., Sitlani, A., Carfi, A.

(2011) EMBO Rep 12: 1300-1305

Released	2011-10-26
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	Low density lipoprotein receptor variant (protein) Proprotein convertase subtilisin/kexin type 9 (protein)
Unique Ligands	CA

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3P5C \| pdb_00003p5c	Download File View File

The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation

Lo Surdo, P., Bottomley, M.J., Calzetta, A., Settembre, E.C., Cirillo, A., Pandit, S., Ni, Y., Hubbard, B., Sitlani, A., Carfi, A.

(2011) EMBO Rep 12: 1300-1305

Released	2011-10-26
Method	X-RAY DIFFRACTION 4.2 Å
Organisms	Homo sapiens
Macromolecule	Low density lipoprotein receptor variant (protein) Proprotein convertase subtilisin/kexin type 9 (protein)
Unique Ligands	CA

1 to 25 of 74 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

Symmetry Type

SCOP Classification

1D8B | pdb_00001d8b

1H5P | pdb_00001h5p

1K1G | pdb_00001k1g

1OQJ | pdb_00001oqj

1VCA | pdb_00001vca

1XWH | pdb_00001xwh

2JW6 | pdb_00002jw6

2K1Q | pdb_00002k1q

2UV0 | pdb_00002uv0

2VQJ | pdb_00002vqj

2VQM | pdb_00002vqm

2VQO | pdb_00002vqo

2VQQ | pdb_00002vqq

2VQV | pdb_00002vqv

2VQW | pdb_00002vqw

2W2M | pdb_00002w2m

2W2N | pdb_00002w2n

2W2O | pdb_00002w2o

2W2P | pdb_00002w2p

2W2Q | pdb_00002w2q

2XTJ | pdb_00002xtj

2Y7S | pdb_00002y7s

2YPV | pdb_00002ypv

3P5B | pdb_00003p5b

3P5C | pdb_00003p5c