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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Pogoryelov, D."

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Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Homo sapiens (9)
	Arthrospira platensis (4)
	Klebsiella pneumoniae (2)
	Saccharolobus solfataricus (2)
	Ilyobacter tartaricus (1)
	Vulcanisaeta distributa DSM 14429 (1)

Taxonomy

	Eukaryota (9)
	Bacteria (7)
	Archaea (3)

Experimental Method

X-RAY DIFFRACTION (19)

Polymer Entity Type

Protein (19)

Refinement Resolution (Å)

	1.5 - 2.0 (7)
	2.0 - 2.5 (10)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (3)
	2015 - 2019 (12)
	2020 - 2024 (2)

Enzyme Classification Name

	Hydrolases (10)
	Transferases (2)

Membrane Protein Annotation

	MemProtMD (2)
	PDBTM (2)
	mpstruc (2)

Symmetry Type

	Asymmetric (8)
	Cyclic (11)

SCOP Classification

	Alpha and beta proteins (a+b) (5)
	Alpha and beta proteins (a/b) (5)
	Artifacts (2)
	All alpha proteins (2)
	All beta proteins (2)

AllSelected

1 to 19 of 19 Structures

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2WGM \| pdb_00002wgm	Download File View File

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase

Meier, T., Pogoryelov, D., Diederichs, K.

(2009) J Mol Biology 391: 498

Released	2009-06-09
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Ilyobacter tartaricus
Macromolecule	ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC (protein)
Unique Ligands	F09, NA

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2WIE \| pdb_00002wie	Download File View File

High-resolution structure of the rotor ring from a proton dependent ATP synthase

Pogoryelov, D., Yildiz, O., Faraldo-Gomez, J.D., Meier, T.

(2009) Nat Struct Mol Biol 16: 1068

Released	2009-09-29
Method	X-RAY DIFFRACTION 2.13 Å
Organisms	Arthrospira platensis
Macromolecule	ATP SYNTHASE C CHAIN (protein)
Unique Ligands	CVM

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2XQS \| pdb_00002xqs	Download File View File

Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

Pogoryelov, D., Krah, A., Langer, J., Yildiz, O., Faraldo-Gomez, J.D., Meier, T.

(2010) Nat Chem Biol 6: 891

Released	2010-10-27
Method	X-RAY DIFFRACTION 3 Å
Organisms	Arthrospira platensis
Macromolecule	ATP SYNTHASE C CHAIN (protein)
Unique Ligands	CVM

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2XQT \| pdb_00002xqt	Download File View File

Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

Pogoryelov, D., Krah, A., Langer, J., Yildiz, O., Faraldo-Gomez, J.D., Meier, T.

(2010) Nat Chem Biol 6: 891

Released	2010-10-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Arthrospira platensis
Macromolecule	ATP SYNTHASE C CHAIN (protein)
Unique Ligands	CVM, DCW

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2XQU \| pdb_00002xqu	Download File View File

Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

Pogoryelov, D., Krah, A., Langer, J., Yildiz, O., Faraldo-Gomez, J.D., Meier, T.

(2010) Nat Chem Biol 6: 891

Released	2010-10-27
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Arthrospira platensis
Macromolecule	ATP SYNTHASE C CHAIN (protein)
Unique Ligands	CVM

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5A5Z \| pdb_00005a5z	Download File View File

Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- lactamases: Strategy To Combat Multidrug-Resistant Bacteria

Klingler, F.M., Wichelhaus, T.A., Frank, D., Cuesta-Bernal, J., El-Delik, J., Mueller, H.F., Sjuts, H., Goettig, S., Koenigs, A., Pogoryelov, D., Proschak, E.

(2015) J Med Chem 58: 3626-3630

Released	2015-07-08
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Klebsiella pneumoniae
Macromolecule	BETA-LACTAMASE NDM-1 (protein)
Unique Ligands	WJZ, ZN

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5AEN \| pdb_00005aen	Download File View File

Structure of human Leukotriene A4 hydrolase in complex with inhibitor dimethyl(2- (4-phenoxyphenoxy)ethyl)amine

Moser, D., Wittmann, S.K., Kramer, J., Blocher, R., Achenbach, J., Pogoryelov, D., Proschak, E.

(2015) J Chem Inf Model 55: 284

Released	2015-02-11
Method	X-RAY DIFFRACTION 1.864 Å
Organisms	Homo sapiens
Macromolecule	LEUKOTRIENE A-4 HYDROLASE (protein)
Unique Ligands	DP8, IMD, YB, ZN

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5AP8 \| pdb_00005ap8	Download File View File

Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from S. solfataricus

Wurm, J.P., Immer, C., Pogoryelov, D., Meyer, B., Koetter, P., Entian, K.-D., Woehnert, J.

(2016) Nucleic Acids Res 44: 4304

Released	2016-04-27
Method	X-RAY DIFFRACTION 2.246 Å
Organisms	Saccharolobus solfataricus
Macromolecule	TSR3 (protein)

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5APG \| pdb_00005apg	Download File View File

Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from Vulcanisaeta distributa

Wurm, J.P., Immer, C., Pogoryelov, D., Meyer, B., Koetter, P., Entian, K.-D., Woehnert, J.

(2016) Nucleic Acids Res 44: 4304

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Vulcanisaeta distributa DSM 14429
Macromolecule	TSR3 (protein)
Unique Ligands	EEM, MES

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5FWQ \| pdb_00005fwq	Download File View File

Apo structure of human Leukotriene A4 hydrolase

Wittmann, S.K., Kalinowsky, L., Kramer, J., Bloecher, R., Steinhilber, D., Pogoryelov, D., Proschak, E., Heering, J.

(2016) Bioorg Med Chem 24: 5243-5248

Released	2016-10-05
Method	X-RAY DIFFRACTION 2.047 Å
Organisms	Homo sapiens
Macromolecule	HUMAN LEUKOTRIENE A4 HYDROLASE (protein)
Unique Ligands	ACT, IMD, YB, ZN

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5MWA \| pdb_00005mwa	Download File View File

human sEH Phosphatase in complex with 3-4-3,4-dichlorophenyl-5-phenyl-1,3-oxazol-2-yl-benzoic-acid

Kramer, J.S., Pogoryelov, D., Sorrell, F.J., Fox, N., Chaikuad, A., Knapp, S., Proschak, E.

(2019) J Med Chem

Released	2018-02-28
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Bifunctional epoxide hydrolase 2 (protein)
Unique Ligands	8S9, MG

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5O7N \| pdb_00005o7n	Download File View File

Beta-lactamase VIM-2 in complex with (2R)-1-(2-Benzyl-3-mercaptopropanoyl)piperidine-2-carboxylic acid

Buettner, D., Kramer, J.S., Pogoryelov, D., Proschak, E.

(2018) ACS Infect Dis 4: 360-372

Released	2018-06-20
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Beta-lactamase VIM-2 (protein)
Unique Ligands	9NK, EDO, FMT, ZN

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6FR2 \| pdb_00006fr2	Download File View File

Soluble epoxide hydrolase in complex with LK864

Kramer, J.S., Pogoryelov, D., Krasavin, M., Proschak, E.

(2018) Bioorg Chem 80: 655-667

Released	2018-09-12
Method	X-RAY DIFFRACTION 2.262 Å
Organisms	Homo sapiens
Macromolecule	Bifunctional epoxide hydrolase 2 (protein)
Unique Ligands	E3N, MG

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6HGV \| pdb_00006hgv	Download File View File

Soluble epoxide hydrolase in complex with talinolol

Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

(2019) ACS Med Chem Lett 10: 899-903

Released	2019-07-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Bifunctional epoxide hydrolase 2 (protein)
Unique Ligands	G3Q, MG

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6HGW \| pdb_00006hgw	Download File View File

Soluble epoxide hydrolase in complex with 2-(4-fluorophenyl)-N-(4-phenoxybenzyl)ethanamine

Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

To be published

Released	2019-08-07
Method	X-RAY DIFFRACTION 2.407 Å
Organisms	Homo sapiens
Macromolecule	Bifunctional epoxide hydrolase 2 (protein)
Unique Ligands	G3W

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6HGX \| pdb_00006hgx	Download File View File

Soluble epoxide hydrolase in complex with 1-(4-((4-(tert-butyl)morpholin-2-yl)methoxy)phenyl)-3-cyclohexylurea

Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

(2019) ACS Med Chem Lett 10: 899-903

Released	2019-07-03
Method	X-RAY DIFFRACTION 2.16 Å
Organisms	Homo sapiens
Macromolecule	Bifunctional epoxide hydrolase 2 (protein)
Unique Ligands	G3T, MG

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6HTJ \| pdb_00006htj	Download File View File

Crystal structure of the translation recovery factor Trf from Sulfolobus solfataricus

Woehnert, J., Pogoryelov, D., Kaiser, M.

(2019) FEBS Open Bio

Released	2019-10-16
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Nucleic-acid-binding protein containing a Zn-ribbon (protein)
Unique Ligands	ZN

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6TBE \| pdb_00006tbe	Download File View File

LC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-hydroxy-3-isopentylbenzamido)-8-methyl-2-oxo-2H-chromen-7-yl)oxy)-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate

Kramer, J.S., Pogoryelov, D., Hartmann, M., Chaikuad, A., Proschak, E.

(2021) J Med Chem 64: 3720-3746

Released	2020-11-18
Method	X-RAY DIFFRACTION 1.67008040045 Å
Organisms	Homo sapiens
Macromolecule	Microtubule-associated proteins 1A/1B light chain 3A (protein)
Unique Ligands	EDO, NOV

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6YL4 \| pdb_00006yl4	Download File View File

Soluble epoxide hydrolase in complex with 3-((R)-3-(1-hydroxyureido)but-1-yn-1-yl)-N-((S)-3-phenyl-3-(4-trifluoromethoxy)phenyl)propyl)benzamide

Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

(2020) J Med Chem 63: 11498-11521

Released	2020-10-21
Method	X-RAY DIFFRACTION 2.001 Å
Organisms	Homo sapiens
Macromolecule	Bifunctional epoxide hydrolase 2 (protein)
Unique Ligands	OWW

1 to 19 of 19 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

2WGM | pdb_00002wgm

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase

2WIE | pdb_00002wie

High-resolution structure of the rotor ring from a proton dependent ATP synthase

2XQS | pdb_00002xqs

Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

2XQT | pdb_00002xqt

Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

2XQU | pdb_00002xqu

Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

5A5Z | pdb_00005a5z

Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- lactamases: Strategy To Combat Multidrug-Resistant Bacteria

5AEN | pdb_00005aen

Structure of human Leukotriene A4 hydrolase in complex with inhibitor dimethyl(2- (4-phenoxyphenoxy)ethyl)amine

5AP8 | pdb_00005ap8

Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from S. solfataricus

5APG | pdb_00005apg

Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from Vulcanisaeta distributa

5FWQ | pdb_00005fwq

Apo structure of human Leukotriene A4 hydrolase

5MWA | pdb_00005mwa

human sEH Phosphatase in complex with 3-4-3,4-dichlorophenyl-5-phenyl-1,3-oxazol-2-yl-benzoic-acid

5O7N | pdb_00005o7n

Beta-lactamase VIM-2 in complex with (2R)-1-(2-Benzyl-3-mercaptopropanoyl)piperidine-2-carboxylic acid

6FR2 | pdb_00006fr2

Soluble epoxide hydrolase in complex with LK864

6HGV | pdb_00006hgv

Soluble epoxide hydrolase in complex with talinolol

6HGW | pdb_00006hgw

Soluble epoxide hydrolase in complex with 2-(4-fluorophenyl)-N-(4-phenoxybenzyl)ethanamine

6HGX | pdb_00006hgx

Soluble epoxide hydrolase in complex with 1-(4-((4-(tert-butyl)morpholin-2-yl)methoxy)phenyl)-3-cyclohexylurea

6HTJ | pdb_00006htj

Crystal structure of the translation recovery factor Trf from Sulfolobus solfataricus

6TBE | pdb_00006tbe

LC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-hydroxy-3-isopentylbenzamido)-8-methyl-2-oxo-2H-chromen-7-yl)oxy)-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate

6YL4 | pdb_00006yl4

Soluble epoxide hydrolase in complex with 3-((R)-3-(1-hydroxyureido)but-1-yn-1-yl)-N-((S)-3-phenyl-3-(4-trifluoromethoxy)phenyl)propyl)benzamide

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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

2WGM | pdb_00002wgm

2WIE | pdb_00002wie

2XQS | pdb_00002xqs

2XQT | pdb_00002xqt

2XQU | pdb_00002xqu

5A5Z | pdb_00005a5z

5AEN | pdb_00005aen

5AP8 | pdb_00005ap8

5APG | pdb_00005apg

5FWQ | pdb_00005fwq

5MWA | pdb_00005mwa

5O7N | pdb_00005o7n

6FR2 | pdb_00006fr2

6HGV | pdb_00006hgv

6HGW | pdb_00006hgw

6HGX | pdb_00006hgx

6HTJ | pdb_00006htj

6TBE | pdb_00006tbe

6YL4 | pdb_00006yl4