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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Bondar, A.N."

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Search Summary

This query matches 30 Structures.

Refinements

Structure Determination Methodology

experimental (30)

Scientific Name of Source Organism

	Halobacterium salinarum NRC-1 (14)
	Bos taurus (8)
	Hyphochytrium catenoides (5)
	synthetic construct (4)
	Thermosynechococcus vestitus BP-1 (3)

Taxonomy

	Archaea (14)
	Eukaryota (13)
	other sequences (4)
	Bacteria (3)

Experimental Method

	X-RAY DIFFRACTION (18)
	ELECTRON MICROSCOPY (12)

Polymer Entity Type

Protein (30)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (1)
	2.0 - 2.5 (15)
	2.5 - 3.0 (2)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)
	4.0 - 4.5 (4)
	> 4.5 (2)

Release Date

	2000 - 2004 (1)
	2015 - 2019 (17)
	2020 - 2024 (9)
	2025 - 2029 (3)

Enzyme Classification Name

	Lyases (7)
	Hydrolases (2)

Membrane Protein Annotation

	MemProtMD (19)
	PDBTM (19)
	mpstruc (14)
	OPM (5)

Symmetry Type

	Cyclic (18)
	Asymmetric (11)

SCOP Classification

Membrane and cell surface proteins and peptides (15)

AllSelected

1 to 25 of 30 Structures

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1U19 \| pdb_00001u19	Download File View File

Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution

Okada, T., Sugihara, M., Bondar, A.N., Elstner, M., Entel, P., Buss, V.

(2004) J Mol Biology 342: 571-583

Released	2004-10-12
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Rhodopsin (protein)
Unique Ligands	HG, HTG, HTO, PLM, RET, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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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

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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

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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

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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

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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

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5G38 \| pdb_00005g38	Download File View File

PsbO subunit of Photosystem II, beta barrel domain at 100K, pH 6

Bommer, M., Bondar, A.N., Zouni, A., Dobbek, H., Dau, H.

(2016) Biochemistry 55: 4626

Released	2016-08-10
Method	X-RAY DIFFRACTION 1.15 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE (protein)
Unique Ligands	CA

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5G39 \| pdb_00005g39	Download File View File

PsbO subunit of Photosystem II, beta barrel domain at 297K, pH 6

Bommer, M., Bondar, A.N., Zouni, A., Dobbek, H., Dau, H.

(2016) Biochemistry 55: 4626

Released	2016-08-10
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE (protein)
Unique Ligands	CA

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5G3A \| pdb_00005g3a	Download File View File

PsbO subunit of Photosystem II, beta barrel domain at 100K, pH 10

Bommer, M., Bondar, A.N., Zouni, A., Dobbek, H., Dau, H.

(2016) Biochemistry 55: 4626

Released	2016-08-10
Method	X-RAY DIFFRACTION 1.224 Å
Organisms	Thermosynechococcus vestitus BP-1
Macromolecule	PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE (protein)
Unique Ligands	CA

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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

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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

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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

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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

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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

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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

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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

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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

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7PD4 \| pdb_00007pd4	Download File View File

structure of Adenylyl cyclase 9 in complex with MANT-GTP

Qi, C., Korkhov, V.M.

(2022) Nat Commun 13: 1045-1045

Released	2022-01-19
Method	ELECTRON MICROSCOPY 4.9 Å
Organisms	Bos taurus
Macromolecule	Adenylate cyclase 9 (protein)

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7PD8 \| pdb_00007pd8	Download File View File

Structure of Adenylyl cyclase 9 in complex with DARPin C4 and MANT-GTP

Qi, C., Korkhov, V.M.

(2022) Nat Commun 13: 1045-1045

Released	2022-01-19
Method	ELECTRON MICROSCOPY 4.2 Å
Organisms	Bos taurus synthetic construct
Macromolecule	Adenylate cyclase 9 (protein) DARPin C4 (protein)

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7PDD \| pdb_00007pdd	Download File View File

Focus refinement of soluble domain of Adenylyl cyclase 9 in complex with DARPin C4 and MANT-GTP

Qi, C., Korkhov, V.M.

(2022) Nat Commun 13: 1045-1045

Released	2022-01-19
Method	ELECTRON MICROSCOPY 4.2 Å
Organisms	Bos taurus synthetic construct
Macromolecule	Adenylate cyclase 9 (protein) DARPin C4 (protein)

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7PDE \| pdb_00007pde	Download File View File

Structure of Adenylyl cyclase 9 in complex with Gs protein alpha subunit and MANT-GTP

Qi, C., Korkhov, V.M.

(2022) Nat Commun 13: 1045-1045

Released	2022-01-19
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Bos taurus
Macromolecule	Adenylate cyclase 9 (protein) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (protein)
Unique Ligands	GSP, MG

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7PDF \| pdb_00007pdf	Download File View File

focus refinement of soluble domain of adenylyl cyclase 9 in complex with Gs protein alpha subunit and MANT-GTP

Qi, C., Korkhov, V.M.

(2022) Nat Commun 13: 1045-1045

Released	2022-01-26
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Bos taurus
Macromolecule	Adenylate cyclase 9 (protein) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (protein)
Unique Ligands	GSP, MG

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7PDG \| pdb_00007pdg	Download File View File

structure of adenylyl cyclase 9 in complex with DARPin C4 and ATP-aS

Qi, C., Korkhov, V.M.

(2022) Nat Commun 13: 1045-1045

Released	2022-01-19
Method	ELECTRON MICROSCOPY 4.3 Å
Organisms	Bos taurus synthetic construct
Macromolecule	Adenylate cyclase 9 (protein) DARPin C4 (protein)