RCSB PDB: Search

1IMJ \| pdb_00001imj	Download File View File

CRYSTAL STRUCTURE OF THE HUMAN CCG1/TAFII250-INTERACTING FACTOR B (CIB)

Padmanabhan, B., Kuzuhara, T., Horikoshi, M.

(2004) J Biological Chem 279: 9615-9624

Released	2002-05-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	CCG1-INTERACTING FACTOR B (protein)
Unique Ligands	SO4

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1IXV \| pdb_00001ixv	Download File View File

Crystal Structure Analysis of homolog of oncoprotein gankyrin, an interactor of Rb and CDK4/6

Padmanabhan, B., Adachi, N., Kataoka, K., Horikoshi, M.

(2004) J Biological Chem 279: 1546-1552

Released	2003-12-16
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Probable 26S proteasome regulatory subunit p28 (protein)

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1KP0 \| pdb_00001kp0	Download File View File

The Crystal Structure Analysis of Creatine Amidinohydrolase from Actinobacillus

Padmanabhan, B., Paehler, A., Horikoshi, M.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1322-1328

Released	2002-07-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Actinobacillus
Macromolecule	CREATINE AMIDINOHYDROLASE (protein)

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1WG0 \| pdb_00001wg0	Download File View File

Structural comparison of Nas6p protein structures in two different crystal forms

Nakamura, Y., Umehara, T., Tanaka, A., Horikoshi, M., Yokoyama, S., Padmanabhan, B., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2005-06-07
Method	X-RAY DIFFRACTION 2.53 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Probable 26S proteasome regulatory subunit p28 (protein)

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1WG3 \| pdb_00001wg3	Download File View File

Structural analysis of yeast nucleosome-assembly factor CIA1p

Padmanabhan, B., Kataoka, K., Umehara, T., Adachi, N., Yokoyama, S., Horikoshi, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) J Biochem 138: 821-829

Released	2005-06-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Anti-silencing protein 1 (protein)

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1X0J \| pdb_00001x0j	Download File View File

Crystal structure analysis of the N-terminal bromodomain of human Brd2

Nakamura, Y., Umehara, T., Shirouzu, M., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-06-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 2 (protein)
Unique Ligands	DTT, MES

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1X2J \| pdb_00001x2j	Download File View File

Structural basis for the defects of human lung cancer somatic mutations in the repression activity of Keap1 on Nrf2

Padmanabhan, B., Tong, K.I., Nakamura, Y., Ohta, T., Scharlock, M., Kobayashi, A., Ohtsuji, M., Kang, M.-I., Yamamoto, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) Mol Cell 21: 689-700

Released	2006-03-07
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mus musculus
Macromolecule	Kelch-like ECH-associated protein 1 (protein)
Unique Ligands	SO4

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1X2R \| pdb_00001x2r	Download File View File

Structural basis for the defects of human lung cancer somatic mutations in the repression activity of Keap1 on Nrf2

Padmanabhan, B., Tong, K.I., Nakamura, Y., Ohta, T., Scharlock, M., Kobayashi, A., Ohtsuji, M., Kang, M.-I., Yamamoto, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) Mol Cell 21: 689-700

Released	2006-03-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mus musculus
Macromolecule	Kelch-like ECH-associated protein 1 (protein) Nuclear factor erythroid 2 related factor 2 (protein)
Unique Ligands	SO4

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2CU9 \| pdb_00002cu9	Download File View File

Crystal structure of Histone chaperone cia1

Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Biological Chem 283: 14022-14031

Released	2006-08-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	Histone chaperone cia1 (protein)
Unique Ligands	PG0

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2DVQ \| pdb_00002dvq	Download File View File

Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide

Nakamura, Y., Umehara, T., Shirouzu, M., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2010) J Biological Chem 285: 7610-7618

Released	2007-08-07
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Homo sapiens Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Macromolecule	Bromodomain-containing protein 2 (protein) histone H4 (protein)

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2DVR \| pdb_00002dvr	Download File View File

Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide

Nakamura, Y., Umehara, T., Shirouzu, M., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2010) J Biological Chem 285: 7610-7618

Released	2007-08-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Macromolecule	bromodomain-containing protein 2 (protein) histone H4 (protein)

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2DVS \| pdb_00002dvs	Download File View File

Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide

Nakamura, Y., Umehara, T., Shirouzu, M., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2010) J Biological Chem 285: 7610-7618

Released	2007-08-07
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Homo sapiens
Macromolecule	bromodomain-containing protein 2 (protein) histone H4 (protein)

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2DVV \| pdb_00002dvv	Download File View File

Crystal structure of the second bromodomain of the human Brd2 protein

Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-08-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Bromodomain-containing protein 2 (protein)
Unique Ligands	EPE

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2DVW \| pdb_00002dvw	Download File View File

Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome

Yokoyama, S., Padmanabhan, B., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Structure 15: 179-189

Released	2007-03-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	26S protease regulatory subunit 6B (protein) 26S proteasome non-ATPase regulatory subunit 10 (protein)

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2DWW \| pdb_00002dww	Download File View File

Crystal structure of Bromodomain-containing protein 4

Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-08-21
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mus musculus
Macromolecule	Bromodomain-containing protein 4 (protein)
Unique Ligands	CL

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2DWZ \| pdb_00002dwz	Download File View File

Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome

Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-08-28
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus Rattus norvegicus
Macromolecule	26S protease regulatory subunit 6B (protein) 26S proteasome non-ATPase regulatory subunit 10 (protein)
Unique Ligands	EPE

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2DX8 \| pdb_00002dx8	Download File View File

Crystal Structure Analysis of the PHD domain of the Transcription Coactivator Pygophus

Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-05-15
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mus musculus
Macromolecule	Pygopus homolog 1 (protein)
Unique Ligands	ZN

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2DYH \| pdb_00002dyh	Download File View File

Crystal structure of the Keap1 protein in complexed with the N-terminal region of the Nrf2 transcription factor

Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Mol Cell Biol 27: 7511-7521

Released	2007-09-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Mus musculus
Macromolecule	Kelch-like ECH-associated protein 1 (protein) Nrf2/Neh2 peptide from Nuclear factor erythroid 2-related factor 2 (protein)
Unique Ligands	SO4

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2DZE \| pdb_00002dze	Download File View File

Crystal structure of histone chaperone Asf1 in complex with a C-terminus of histone H3

Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-10-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Schizosaccharomyces pombe Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Macromolecule	10-mer peptide from Histone H3.1/H3.2 (protein) Histone chaperone cia1 (protein)
Unique Ligands	PGE

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2DZN \| pdb_00002dzn	Download File View File

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3

Yokoyama, S., Padmanabhan, B., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) Biochem Biophys Res Commun 359: 503-509

Released	2007-07-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	26S protease regulatory subunit 6B homolog (protein) Probable 26S proteasome regulatory subunit p28 (protein)

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2DZO \| pdb_00002dzo	Download File View File

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3

Nakamura, Y., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-10-16
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	26S protease regulatory subunit 6B homolog (protein) Probable 26S proteasome regulatory subunit p28 (protein)

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2E3K \| pdb_00002e3k	Download File View File

Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 peptide

Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-12-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Macromolecule	15-mer peptide from Histone H4 (protein) Bromodomain-containing protein 2 (protein)

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2JNS \| pdb_00002jns	Download File View File

Solution structure of the Bromodomain-containing protein 4 ET domain

Lin, Y.J., Padmanabhan, B., Yokoyama, S., Guntert, P., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-02-05
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Bromodomain-containing protein 4 (protein)

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2M62 \| pdb_00002m62	Download File View File

Solution Structure of a Chi/Lambda Conotoxin fron Conus araneosus

Sarma, S.P., Ganesan, S., Gowd K, H., Padmanabhan, B.

To be published

Released	2014-04-16
Method	SOLUTION NMR
Organisms	Conus araneosus
Macromolecule	Chi-conotoxin-like Ar1248 (protein)

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2YXD \| pdb_00002yxd	Download File View File

Crystal Structure of Cobalamin biosynthesis precorrin 8W decarboxylase (cbiT)

Padmanabhan, B., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-10-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanocaldococcus jannaschii DSM 2661
Macromolecule	Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating] (protein)
Unique Ligands	MES, SO4

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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

1IMJ | pdb_00001imj

1IXV | pdb_00001ixv

1KP0 | pdb_00001kp0

1WG0 | pdb_00001wg0

1WG3 | pdb_00001wg3

1X0J | pdb_00001x0j

1X2J | pdb_00001x2j

1X2R | pdb_00001x2r

2CU9 | pdb_00002cu9

2DVQ | pdb_00002dvq

2DVR | pdb_00002dvr

2DVS | pdb_00002dvs

2DVV | pdb_00002dvv

2DVW | pdb_00002dvw

2DWW | pdb_00002dww

2DWZ | pdb_00002dwz

2DX8 | pdb_00002dx8

2DYH | pdb_00002dyh

2DZE | pdb_00002dze

2DZN | pdb_00002dzn

2DZO | pdb_00002dzo

2E3K | pdb_00002e3k

2JNS | pdb_00002jns

2M62 | pdb_00002m62

2YXD | pdb_00002yxd