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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = DD9

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Search Summary

This query matches 72 Structures.

Refinements

Structure Determination Methodology

experimental (72)

Scientific Name of Source Organism

	Halobacterium salinarum NRC-1 (32)
	Homo sapiens (7)
	Tetronarce californica (7)
	Halorubrum sodomense (6)
	Halobacterium salinarum (5)
	Aequorea victoria (3)
	Mus musculus (3)
	Escherichia coli K-12 (2)
	Saccharomyces cerevisiae (2)
	Cereibacter sphaeroides 2.4.1 (1)

More...

Taxonomy

	Archaea (45)
	Eukaryota (19)
	Bacteria (7)
	Riboviria (1)
	Varidnaviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (54)
	ELECTRON MICROSCOPY (18)

Polymer Entity Type

Protein (72)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (25)
	2.0 - 2.5 (23)
	2.5 - 3.0 (10)
	3.0 - 3.5 (4)
	3.5 - 4.0 (6)
	4.0 - 4.5 (1)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (2)
	2015 - 2019 (43)
	2020 - 2024 (25)

Enzyme Classification Name

	Transferases (3)
	Isomerases (1)
	Oxidoreductases (1)

Membrane Protein Annotation

	PDBTM (65)
	MemProtMD (62)
	mpstruc (57)
	OPM (14)

Symmetry Type

	Asymmetric (35)
	Cyclic (36)
	Dihedral (1)

SCOP Classification

	Membrane and cell surface proteins and peptides (43)
	All beta proteins (1)

AllSelected

1 to 25 of 72 Structures

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Explore in 3D

3ATR \| pdb_00003atr	Download File View File

Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius co-crystallized with its ligand

Fujihashi, M., Sasaki, D., Iwata, Y., Yoshimura, T., Hemmi, H., Miki, K.

(2011) J Mol Biology 409: 543-557

Released	2011-05-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Sulfolobus acidocaldarius
Macromolecule	Conserved Archaeal protein (protein)
Unique Ligands	DD9, FDA, PPV

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3HAP \| pdb_00003hap	Download File View File

Crystal structure of bacteriorhodopsin mutant L111A crystallized from bicelles

Joh, N.H., Yang, D., Bowie, J.U.

(2009) J Am Chem Soc 131: 10846-10847

Released	2009-09-22
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	CPS, D10, D12, DD9, HP6, R16, RET

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3HAQ \| pdb_00003haq	Download File View File

Crystal structure of bacteriorhodopsin mutant I148A crystallized from bicelles

Joh, N.H., Yang, D., Bowie, J.U.

(2009) J Am Chem Soc 131: 10846-10847

Released	2009-09-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	CPS, D10, D12, DD9, HP6, R16, RET

Explore in 3D

4DX5 \| pdb_00004dx5	Download File View File

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

Eicher, T., Cha, H., Seeger, M.A., Brandstaetter, L., El-Delik, J., Bohnert, J.A., Kern, W.V., Verrey, F., Gruetter, M.G., Diederichs, K., Pos, K.M.

(2012) Proc Natl Acad Sci U S A 109: 5687-5692

Released	2012-05-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli K-12 synthetic construct
Macromolecule	Acriflavine resistance protein B (protein) DARPIN (protein)
Unique Ligands	C14, D10, D12, DD9, GOL, HEX, LMT, LMU, MIY, OCT, SO4, UND

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4Y9H \| pdb_00004y9h	Download File View File

The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles

Saiki, H., Sugiyama, S., Kakinouchi, K., Kawatake, S., Hanashima, S., Matsumori, N., Murata, M.

To be published

Released	2016-02-17
Method	X-RAY DIFFRACTION 1.43 Å
Organisms	Halobacterium salinarum R1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	D10, D12, DD9, HP6, PO4, R16, RET

Explore in 3D

5B34 \| pdb_00005b34	Download File View File

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Mizohata, E., Nakane, T.

(2016) Proc Natl Acad Sci U S A 113: 13039-13044

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	4QL, D10, D12, DD9, HP6, OCT, R16, RET

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5B35 \| pdb_00005b35	Download File View File

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Mizohata, E., Nakane, T., Suzuki, M.

(2016) Proc Natl Acad Sci U S A 113: 13039-13044

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Halobacterium salinarum
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	4QM, D10, D12, DD9, HP6, OCT, R16, RET

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5B6V \| pdb_00005b6v	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: resting state structure

Nango, E., Royant, A., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5B6W \| pdb_00005b6w	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 16 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5B6X \| pdb_00005b6x	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 760 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5B6Y \| pdb_00005b6y	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 36.2 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5B6Z \| pdb_00005b6z	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 1.725 ms us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2H \| pdb_00005h2h	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 40 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2I \| pdb_00005h2i	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 110 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2J \| pdb_00005h2j	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 290 ns after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2K \| pdb_00005h2k	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 2 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2L \| pdb_00005h2l	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 5.25 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2M \| pdb_00005h2m	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 13.8 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2N \| pdb_00005h2n	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 95.2 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2O \| pdb_00005h2o	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 250 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5H2P \| pdb_00005h2p	Download File View File

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 657 us after photoexcitation

Royant, A., Nango, E., Nakane, T., Tanaka, T., Arima, T., Neutze, R., Iwata, S.

(2016) Science 354: 1552-1557

Released	2016-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

Explore in 3D

5KYM \| pdb_00005kym	Download File View File

Crystal Structure of the 1-acyl-sn-glycerophosphate (LPA) acyltransferase, PlsC, from Thermotoga maritima

Robertson, R.M., Yao, J., Gajewski, S., Kumar, G., Martin, E.W., Rock, C.O., White, S.W.

(2017) Nat Struct Mol Biol 24: 666-671

Released	2017-07-26
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermotoga maritima MSB8
Macromolecule	1-acyl-sn-glycerol-3-phosphate acyltransferase (protein)
Unique Ligands	DD9, HGX, LMT

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5LRI \| pdb_00005lri	Download File View File

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH GLUL212 REPLACED WITH TRP (CHAIN L, EL212W)

Fyfe, P.K., Jones, M.R.

(2016) Biochim Biophys Acta 1857: 1925-1934

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Cereibacter sphaeroides 2.4.1
Macromolecule	Reaction center protein H chain (protein) Reaction center protein L chain (protein) Reaction center protein M chain (protein)
Unique Ligands	BCL, BPH, CDL, DD9, FE, LDA, SPN, U10

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5NC5 \| pdb_00005nc5	Download File View File

Crystal structure of AcrBZ in complex with antibiotic puromycin

Du, D., Luisi, B.

(2017) Elife 6:

Released	2017-04-12
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Escherichia coli Escherichia coli K-12 Escherichia coli O157:H7
Macromolecule	DARPin (protein) Multidrug efflux pump accessory protein AcrZ (protein) Multidrug efflux pump subunit AcrB (protein)
Unique Ligands	D10, D12, DD9, HEX, LMT, PUY

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6GA1 \| pdb_00006ga1	Download File View File

Bacteriorhodopsin, dark state, cell 1

Nass Kovacs, G., Colletier, J.-P., Gruenbein, M.L., Stensitzki, T., Batyuk, A., Carbajo, S., Doak, R.B., Ehrenberg, D., Foucar, L., Gasper, R., Gorel, A., Hilpert, M., Kloos, M., Koglin, J., Reinstein, J., Roome, C.M., Schlesinger, R., Seaberg, M., Shoeman, R.L., Stricker, M., Boutet, S., Haacke, S., Heberle, J., Domratcheva, T., Barends, T.R.M., Schlichting, I.

(2019) Nat Commun 10: 3177-3177

Released	2019-04-24
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Halobacterium salinarum NRC-1
Macromolecule	Bacteriorhodopsin (protein)
Unique Ligands	C14, D10, DD9, HP6, L2P, MYS, OCT, RET, TRD, UND

1 to 25 of 72 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

3ATR | pdb_00003atr

3HAP | pdb_00003hap

3HAQ | pdb_00003haq

4DX5 | pdb_00004dx5

4Y9H | pdb_00004y9h

5B34 | pdb_00005b34

5B35 | pdb_00005b35

5B6V | pdb_00005b6v

5B6W | pdb_00005b6w

5B6X | pdb_00005b6x

5B6Y | pdb_00005b6y

5B6Z | pdb_00005b6z

5H2H | pdb_00005h2h

5H2I | pdb_00005h2i

5H2J | pdb_00005h2j

5H2K | pdb_00005h2k

5H2L | pdb_00005h2l

5H2M | pdb_00005h2m

5H2N | pdb_00005h2n

5H2O | pdb_00005h2o

5H2P | pdb_00005h2p

5KYM | pdb_00005kym

5LRI | pdb_00005lri

5NC5 | pdb_00005nc5

6GA1 | pdb_00006ga1