RCSB PDB: Search

2A4G \| pdb_00002a4g	Download File View File

Hepatitis C Protease NS3-4A serine protease with Ketoamide Inhibitor SCH225724 Bound

Arasappan, A., Njoroge, F.G., Chan, T.Y., Bennett, F., Bogen, S.L., Chen, K., Gu, H., Hong, L., Jao, E., Liu, Y.T., Lovey, R.G., Parekh, T., Pike, R.E., Pinto, P., Santhanam, B., Venkatraman, S., Vaccaro, H., Wang, H., Yang, X., Zhu, Z., Mckittrick, B., Saksena, A.K., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Ingram, R., Malcolm, B., Prongay, A.J., Yao, N., Marten, B., Madison, V., Kemp, S., Levy, O., Lim-Wilby, M., Tamura, S., Ganguly, A.K.

(2005) Bioorg Med Chem Lett 15: 4180-4184

Released	2006-07-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Hepacivirus hominis Hepatitis C virus subtype 1b
Macromolecule	NS3 protease/helicase (protein) NS4a peptide (protein)
Unique Ligands	UNH, ZN

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2A4Q \| pdb_00002a4q	Download File View File

HCV NS3 protease with NS4a peptide and a covalently bound macrocyclic ketoamide compound.

Chen, K.X., Njoroge, F.G., Prongay, A., Pichardo, J., Madison, V., Girijavallabhan, V.

(2005) Bioorg Med Chem Lett 15: 4475-4478

Released	2006-07-04
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Hepacivirus hominis
Macromolecule	NS3 protease/helicase' (protein) NS4a peptide (protein)
Unique Ligands	BME, FNH, ZN

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2A4R \| pdb_00002a4r	Download File View File

HCV NS3 Protease Domain with a Ketoamide Inhibitor Covalently bound.

Bogen, S., Saksena, A.K., Arasappan, A., Gu, H., Njoroge, F.G., Girijavallabhan, V., Pichardo, J., Butkiewicz, N., Prongay, A., Madison, V.

(2005) Bioorg Med Chem Lett 15: 4515-4519

Released	2006-07-04
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Hepacivirus hominis Hepatitis C virus genotype 1a (isolate H77)
Macromolecule	NS3 protease/helicase (protein) Ns4a peptide (protein)
Unique Ligands	BNH, ZN

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2GVF \| pdb_00002gvf	Download File View File

HCV NS3-4A protease domain complexed with a macrocyclic ketoamide inhibitor, SCH419021

Arasappan, A., Njoroge, F.G., Chen, K.X., Venkatraman, S., Parekh, T.N., Gu, H., Pichardo, J., Butkiewicz, N., Prongay, A., Madison, V., Girijavallabhan, V.

(2006) Bioorg Med Chem Lett 16: 3960-3965

Released	2007-01-23
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Hepacivirus hominis Hepatitis C virus genotype 1a (isolate 1)
Macromolecule	Polyprotein (protein) polyprotein (protein)
Unique Ligands	NHN, ZN

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2OBO \| pdb_00002obo	Download File View File

Structure of HEPATITIS C VIRAL NS3 protease domain complexed with NS4A peptide and ketoamide SCH476776

Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers Jr., J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R., Arasappan, A., Bennett, F., Bogen, S.F., Chen, K., Jao, E., Liu, Y., Love, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.

(2007) J Med Chem 50: 2310-2318

Released	2007-07-31
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Hepacivirus hominis Hepatitis C virus subtype 1b
Macromolecule	HCV NS3 protease (protein) HCV NS4A peptide (protein)
Unique Ligands	BME, HUD, ZN

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2OBQ \| pdb_00002obq	Download File View File

Discovery of the HCV NS3/4A Protease Inhibitor SCH503034. Key Steps in Structure-Based Optimization

Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers Jr., J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R., Arasappan, A., Bennett, F., Bogen, S.F., Chen, K., Jao, E., Liu, Y., Love, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.

(2007) J Med Chem 50: 2310-2318

Released	2007-07-31
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Hepacivirus hominis Hepatitis C virus genotype 1a (isolate H77)
Macromolecule	Hepatitis C virus (protein)
Unique Ligands	ZN

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2OC0 \| pdb_00002oc0	Download File View File

Structure of NS3 complexed with a ketoamide inhibitor SCh491762

Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers Jr., J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R., Arasappan, A., Bennett, F., Bogen, S.F., Chen, K., Jao, E., Liu, Y., Love, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.

(2007) J Med Chem 50: 2310-2318

Released	2007-07-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Hepacivirus hominis Hepatitis C virus genotype 1a (isolate H77)
Macromolecule	Hepatitis C Virus (protein) Hepatitis C virus (protein)
Unique Ligands	BME, HU1, ZN

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2OC1 \| pdb_00002oc1	Download File View File

Structure of the HCV NS3/4A Protease Inhibitor CVS4819

Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers Jr., J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R., Arasappan, A., Bennett, F., Bogen, S.F., Chen, K., Jao, E., Liu, Y., Love, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.

(2007) J Med Chem 50: 2310-2318

Released	2007-07-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Hepacivirus hominis Hepatitis C virus genotype 1a (isolate H77)
Macromolecule	Hepatitis C virus (protein)
Unique Ligands	HU2, ZN

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2OC7 \| pdb_00002oc7	Download File View File

Structure of Hepatitis C Viral NS3 protease domain complexed with NS4A peptide and ketoamide SCH571696

Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers Jr., J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R., Arasappan, A., Bennett, F., Bogen, S.F., Chen, K., Jao, E., Liu, Y., Love, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.

(2007) J Med Chem 50: 2310-2318

Released	2007-07-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Hepacivirus hominis Hepatitis C virus genotype 1a (isolate H77)
Macromolecule	Hepatitis C Virus (protein)
Unique Ligands	BME, HU4, ZN

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2OC8 \| pdb_00002oc8	Download File View File

Structure of Hepatitis C Viral NS3 protease domain complexed with NS4A peptide and ketoamide SCH503034

Prongay, A.J., Guo, Z., Yao, N., Fischmann, T., Strickland, C., Myers, J., Weber, P.C., Malcolm, B., Beyer, B.M., Ingram, R., Pichardo, J., Hong, Z., Prosise, W.W., Ramanathan, L., Taremi, S.S., Yarosh-Tomaine, T., Zhang, R., Senior, M., Yang, R.S., Arasappan, A., Bennett, F., Bogen, S.L., Chen, K., Jao, E., Liu, Y.T., Lovey, R.G., Saksena, A.K., Venkatraman, S., Girijavallabhan, V., Njoroge, F.G., Madison, V.

(2007) J Med Chem 50: 2310-2318

Released	2007-07-31
Method	X-RAY DIFFRACTION 2.66 Å
Organisms	Hepacivirus hominis Hepatitis C virus genotype 1a (isolate H77)
Macromolecule	Hepatitis C virus (protein)
Unique Ligands	BME, U5G, ZN

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3J92 \| pdb_00003j92	Download File View File

Structure and assembly pathway of the ribosome quality control complex

Shao, S., Brown, A., Santhanam, B., Hegde, R.S.

(2015) Mol Cell 57: 433-444

Released	2015-01-21
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Homo sapiens Oryctolagus cuniculus Sus scrofa
Macromolecule	Unique protein chains: 47 Unique nucleic acid chains: 4
Unique Ligands	MG, ZN

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5HAF \| pdb_00005haf	Download File View File

Structure of Salmonella enterica effector protein SseL

Pruneda, J.N., Komander, D.

(2016) Mol Cell 63: 261-276

Released	2016-07-27
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Deubiquitinase SseL (protein)
Unique Ligands	K

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5HAG \| pdb_00005hag	Download File View File

Structure of Chlamydia trachomatis effector protein ChlaDUB1

Pruneda, J.N., Komander, D.

(2016) Mol Cell 63: 261-276

Released	2016-07-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Chlamydia trachomatis
Macromolecule	Deubiquitinase and deneddylase Dub1 (protein)
Unique Ligands	GOL

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5HAM \| pdb_00005ham	Download File View File

Structure of Rickettsia bellii effector protein RickCE

Pruneda, J.N., Komander, D.

(2016) Mol Cell 63: 261-276

Released	2016-07-27
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Rickettsia bellii
Macromolecule	RickCE (protein)

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5JP1 \| pdb_00005jp1	Download File View File

Structure of Xanthomonas campestris effector protein XopD bound to tomato SUMO

Pruneda, J.N., Komander, D.

(2016) Mol Cell 63: 261-276

Released	2016-07-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Solanum lycopersicum Xanthomonas euvesicatoria pv. vesicatoria str. 85-10
Macromolecule	Small ubiquitin-related modifier (protein) Xanthomonas outer protein D (protein)
Unique Ligands	D1D, MLI

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5JP3 \| pdb_00005jp3	Download File View File

Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin

Pruneda, J.N., Komander, D.

(2016) Mol Cell 63: 261-276

Released	2016-07-27
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens Xanthomonas euvesicatoria pv. vesicatoria str. 85-10
Macromolecule	Polyubiquitin-B (protein) Xanthomonas outer protein D (protein)

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5NP0 \| pdb_00005np0	Download File View File

Closed dimer of human ATM (Ataxia telangiectasia mutated)

Baretic, D., Pollard, H.K., Fisher, D.I., Johnson, C.M., Santhanam, B., Truman, C.M., Kouba, T., Fersht, A.R., Phillips, C., Williams, R.L.

(2017) Sci Adv 3: e1700933-e1700933

Released	2017-05-17
Method	ELECTRON MICROSCOPY 5.7 Å
Organisms	Homo sapiens
Macromolecule	Serine-protein kinase ATM (protein)

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5NP1 \| pdb_00005np1	Download File View File

Open protomer of human ATM (Ataxia telangiectasia mutated)

Baretic, D., Pollard, H.K., Fisher, D.I., Johnson, C.M., Santhanam, B., Truman, C.M., Kouba, T., Fersht, A.R., Phillips, C., Williams, R.L.

(2017) Sci Adv 3: e1700933-e1700933

Released	2017-05-17
Method	ELECTRON MICROSCOPY 5.7 Å
Organisms	Homo sapiens
Macromolecule	Serine-protein kinase ATM (protein)

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6EOJ \| pdb_00006eoj	Download File View File

PolyA polymerase module of the cleavage and polyadenylation factor (CPF) from Saccharomyces cerevisiae

Casanal, A., Kumar, A., Hill, C.H., Emsley, P., Passmore, L.A.

(2017) Science 358: 1056-1059

Released	2017-11-15
Method	ELECTRON MICROSCOPY 3.55 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Polyadenylation factor subunit 2,Polyadenylation factor subunit 2 (protein) Protein CFT1 (protein) mRNA 3'-end-processing protein YTH1 (protein)
Unique Ligands	ZN

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6GZS \| pdb_00006gzs	Download File View File

Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin

Pruneda, J.N., Komander, D.

(2018) Nat Microbiol 3: 1377-1384

Released	2018-11-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Chlamydia trachomatis L2/434/Bu Homo sapiens
Macromolecule	Deubiquitinase and deneddylase Dub1 (protein) Polyubiquitin-B (protein)
Unique Ligands	AYE, GOL, SO4

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6GZT \| pdb_00006gzt	Download File View File

Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to Coenzyme A

Pruneda, J.N., Komander, D.

(2018) Nat Microbiol 3: 1377-1384

Released	2018-11-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Chlamydia trachomatis
Macromolecule	Deubiquitinase and deneddylase Dub1 (protein)
Unique Ligands	COA, GOL, SO4

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6GZU \| pdb_00006gzu	Download File View File

Structure of Chlamydia abortus effector protein ChlaDUB

Pruneda, J.N., Komander, D.

(2018) Nat Microbiol 3: 1377-1384

Released	2018-11-14
Method	X-RAY DIFFRACTION 1.47 Å
Organisms	Chlamydia abortus
Macromolecule	Conserved membrane protein (protein)
Unique Ligands	GOL, ZN

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6S6A \| pdb_00006s6a	Download File View File

Crystal structure of RagA-Q66L/RagC-T90N GTPase heterodimer complex

Anandapadamanaban, M., Masson, G.R., Perisic, O., Kaufman, J., Williams, R.L.

(2019) Science 366: 203-210

Released	2019-10-16
Method	X-RAY DIFFRACTION 2.63 Å
Organisms	Homo sapiens
Macromolecule	Ras-related GTP-binding protein A (protein) Ras-related GTP-binding protein C (protein)
Unique Ligands	9JE, GDP, GTP, MG

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6S6D \| pdb_00006s6d	Download File View File

Crystal structure of RagA-Q66L-GTP/RagC-S75N-GDP GTPase heterodimer complex

Anandapadamanaban, M., Masson, G.R., Perisic, O., Kaufman, J., Williams, R.L.

(2019) Science 366: 203-210

Released	2019-10-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Ras-related GTP-binding protein A (protein) Ras-related GTP-binding protein C (protein)
Unique Ligands	9JE, GDP, GTP, MG

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6SB0 \| pdb_00006sb0	Download File View File

cryo-EM structure of mTORC1 bound to PRAS40-fused active RagA/C GTPases

Anandapadamanaban, M., Berndt, A., Masson, G.R., Perisic, O., Williams, R.L.

(2019) Science 366: 203-210

Released	2019-10-16
Method	ELECTRON MICROSCOPY 5.5 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6
Unique Ligands	GDP, GTP

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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

2A4G | pdb_00002a4g

2A4Q | pdb_00002a4q

2A4R | pdb_00002a4r

2GVF | pdb_00002gvf

2OBO | pdb_00002obo

2OBQ | pdb_00002obq

2OC0 | pdb_00002oc0

2OC1 | pdb_00002oc1

2OC7 | pdb_00002oc7

2OC8 | pdb_00002oc8

3J92 | pdb_00003j92

5HAF | pdb_00005haf

5HAG | pdb_00005hag

5HAM | pdb_00005ham

5JP1 | pdb_00005jp1

5JP3 | pdb_00005jp3

5NP0 | pdb_00005np0

5NP1 | pdb_00005np1

6EOJ | pdb_00006eoj

6GZS | pdb_00006gzs

6GZT | pdb_00006gzt

6GZU | pdb_00006gzu

6S6A | pdb_00006s6a

6S6D | pdb_00006s6d

6SB0 | pdb_00006sb0