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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Clarke, D.J."

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Search Summary

This query matches 25 Structures.

Refinements

Structure Determination Methodology

experimental (25)

Scientific Name of Source Organism

	Rhodospirillum rubrum (5)
	Aquifex aeolicus (3)
	Haliangium ochraceum DSM 14365 (3)
	Lachnoclostridium phytofermentans (2)
	Rhodospirillum rubrum ATCC 11170 (2)
	Sphingomonas paucimobilis (2)
	Burkholderia pseudomallei K96243 (1)
	Escherichia coli (1)
	Haliangium ochraceum (1)
	Lachnoclostridium phytofermentans ISDg (1)

More...

Taxonomy

	Bacteria (23)
	Archaea (1)
	Eukaryota (1)

Experimental Method

	X-RAY DIFFRACTION (22)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (25)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (3)
	2.0 - 2.5 (14)
	2.5 - 3.0 (6)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (4)
	2015 - 2019 (11)
	2020 - 2024 (7)

Enzyme Classification Name

	Oxidoreductases (12)
	Transferases (5)
	Ligases (3)

Symmetry Type

	Dihedral (11)
	Asymmetric (6)
	Cyclic (7)
	Icosahedral (1)

SCOP Classification

	All alpha proteins (8)
	Artifacts (7)

AllSelected

1 to 25 of 25 Structures

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2X8U \| pdb_00002x8u	Download File View File

Sphingomonas wittichii Serine palmitoyltransferase

Raman, M.C.C., Johnson, K.A., Campopiano, D.J., Naismith, J.H.

(2010) Biopolymers 93: 811

Released	2010-03-23
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Rhizorhabdus wittichii RW1
Macromolecule	SERINE PALMITOYLTRANSFERASE (protein)
Unique Ligands	PLP

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2XBN \| pdb_00002xbn	Download File View File

Inhibition of the PLP-dependent enzyme serine palmitoyltransferase by cycloserine: evidence for a novel decarboxylative mechanism of inactivation

Lowther, J., Yard, B.A., Johnson, K.A., Carter, L.G., Bhat, V.T., Raman, M.C.C., Clarke, D.J., Ramakers, B., McMahon, S.A., Naismith, J.H., Campopiano, D.J.

(2010) Mol Biosyst 6: 1682

Released	2010-05-19
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Sphingomonas paucimobilis
Macromolecule	SERINE PALMITOYLTRANSFERASE (protein)
Unique Ligands	MG, PMP

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3EFR \| pdb_00003efr	Download File View File

Biotin protein ligase R40G mutant from Aquifex aeolicus in complex with biotin

Tron, C.M., McNae, I.W., Walkinshaw, M.D., Baxter, R.L., Campopiano, D.J.

(2009) J Mol Biology 387: 129-146

Released	2009-06-09
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Aquifex aeolicus
Macromolecule	Biotin [acetyl-CoA-carboxylase] ligase (protein)
Unique Ligands	BTN, SO4

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3EFS \| pdb_00003efs	Download File View File

Biotin protein ligase from Aquifex aeolicus in complex with biotin and ATP

Tron, C.M., McNae, I.W., Walkinshaw, M.D., Baxter, R.L., Campopiano, D.J.

(2009) J Mol Biology 387: 129-146

Released	2009-06-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aquifex aeolicus
Macromolecule	Biotin [acetyl-CoA-carboxylase] ligase (protein)
Unique Ligands	ATP, BTN, SO4

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3FJP \| pdb_00003fjp	Download File View File

Apo structure of Biotin protein ligase from Aquifex aeolicus

McNae, I.W., Tron, C.M., Baxter, R.L., Walkinshaw, M.D., Campopiano, D.J.

(2009) J Mol Biology 387: 129-146

Released	2009-06-09
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aquifex aeolicus
Macromolecule	Biotin [acetyl-CoA-carboxylase] ligase (protein)
Unique Ligands	SO4

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4BMK \| pdb_00004bmk	Download File View File

Serine Palmitoyltransferase K265A from S. paucimobilis with bound PLP- Myriocin Aldimine

Wadsworth, J.M., Clarke, D.J., McMahon, S.A., Beattie, A.E., Lowther, J., Dunn, T.M., Naismith, J.H., Campopiano, D.J.

(2013) J Am Chem Soc 135: 14276

Released	2013-09-04
Method	X-RAY DIFFRACTION 1.62 Å
Organisms	Sphingomonas paucimobilis
Macromolecule	SERINE PALMITOYLTRANSFERASE (protein)
Unique Ligands	GOL, MYB, PLP

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4C3S \| pdb_00004c3s	Download File View File

Structure of a propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment

Marles-Wright, J., Crawshaw, A., Ang, T.F., Altenbach, K.

(2016) Sci Rep 6: 22108

Released	2013-09-11
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Lachnoclostridium phytofermentans
Macromolecule	ALDEHYDE DEHYDROGENASE (protein)
Unique Ligands	NAD, SO4

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4TQX \| pdb_00004tqx	Download File View File

Molecular Basis of Streptococcus mutans Sortase A Inhibition by Chalcone.

Wallock-Richards, D.J., Marles-Wright, J., Clarke, D.J., Maitra, A., Dodds, M., Hanley, B., Campopiano, D.J.

(2015) Chem Commun (Camb) 51: 10483-10485

Released	2015-05-20
Method	X-RAY DIFFRACTION 1.37 Å
Organisms	Streptococcus mutans
Macromolecule	Sortase (protein)
Unique Ligands	ACY, PG4, SO4

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5DA5 \| pdb_00005da5	Download File View File

Crystal structure of Rhodospirillum rubrum Rru_A0973

He, D., Vanden Hehier, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.

(2016) Elife 5:

Released	2016-08-10
Method	X-RAY DIFFRACTION 2.064 Å
Organisms	Rhodospirillum rubrum
Macromolecule	Rru_A0973 (protein)
Unique Ligands	CA, FE, GOA

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5DBV \| pdb_00005dbv	Download File View File

Structure of a C269A mutant of propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment

Tuck, L.R., Altenbach, K., Ang, T.F., Crawshaw, A.D., Campopiano, D.J., Clarke, D.J., Marles-Wright, J.

(2016) Sci Rep 6: 22108-22108

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Lachnoclostridium phytofermentans ISDg
Macromolecule	Aldehyde Dehydrogenase (protein)
Unique Ligands	ACT, COA, SO4

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5DRU \| pdb_00005dru	Download File View File

Structure of His387Ala mutant of the propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment

Tuck, L.R., Altenbach, K., Fu, A.T., Crawshaw, A.D., Campopiano, D.J., Clarke, D.J., Marles-Wright, J.

(2016) Sci Rep 6: 22108-22108

Released	2016-03-16
Method	X-RAY DIFFRACTION 2.083 Å
Organisms	Lachnoclostridium phytofermentans
Macromolecule	Aldehyde Dehydrogenase (protein)
Unique Ligands	SO4

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5K1R \| pdb_00005k1r	Download File View File

Structure of Burkholderia pseudomallei K96243 sphingosine-1-phosphate lyase Bpss2021

Mclean, C.J., Campopiano, D.J., Marles-Wright, J.

(2017) J Lipid Res 58: 137-150

Released	2016-11-02
Method	X-RAY DIFFRACTION 2.104 Å
Organisms	Burkholderia pseudomallei K96243
Macromolecule	Burkholderia pseudomallei sphingosine-1-phosphate lyase Bpss2021 (protein)
Unique Ligands	PLP

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5L89 \| pdb_00005l89	Download File View File

Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A

He, D., Hughes, S., Vanden-Hehir, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.

(2016) Elife 5:

Released	2016-08-31
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Rhodospirillum rubrum
Macromolecule	Rru_A0973 (protein)
Unique Ligands	CA

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5L8B \| pdb_00005l8b	Download File View File

Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E62A

He, D., Hughes, S., Vanden-Hehir, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.

(2016) Elife 5:

Released	2016-08-31
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Rhodospirillum rubrum
Macromolecule	Uncharacterized protein (protein)
Unique Ligands	CA

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5L8F \| pdb_00005l8f	Download File View File

Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A, E62A, H65A.

He, D., Hughes, S., Vanden-Hehir, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.

To be published

Released	2017-06-21
Method	X-RAY DIFFRACTION 2.247 Å
Organisms	Rhodospirillum rubrum ATCC 11170
Macromolecule	Rru_A0973 (protein)
Unique Ligands	MG, PGE

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5L8G \| pdb_00005l8g	Download File View File

Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant H65A

He, D., Hughes, S., Vanden-Hehir, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.

(2016) Elife 5:

Released	2016-08-31
Method	X-RAY DIFFRACTION 2.974 Å
Organisms	Rhodospirillum rubrum
Macromolecule	Uncharacterized protein (protein)
Unique Ligands	CA

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5N5E \| pdb_00005n5e	Download File View File

Crystal structure of encapsulated ferritin domain from Pyrococcus furiosus PFC_05175

Marles-Wright, J., He, D.

(2019) Biochem J 476: 975-989

Released	2018-01-24
Method	X-RAY DIFFRACTION 2.026 Å
Organisms	Pyrococcus furiosus COM1
Macromolecule	PFC_05175 (protein)
Unique Ligands	FE

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5N5F \| pdb_00005n5f	Download File View File

Crystal structure of Haliangium ochraceum encapsulated ferritin

Marles-Wright, J., He, D.

(2019) Biochem J 476: 975-989

Released	2018-01-24
Method	X-RAY DIFFRACTION 2.057 Å
Organisms	Haliangium ochraceum
Macromolecule	encapsulated ferritin (protein)
Unique Ligands	NA

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6SUW \| pdb_00006suw	Download File View File

Crystal structure of Rhodospirillum rubrum Rru_A0973 E31A variant

Marles-Wright, J., He, D.

(2020) J Biological Chem 295: 15511-15526

Released	2020-09-23
Method	X-RAY DIFFRACTION 2.66 Å
Organisms	Rhodospirillum rubrum ATCC 11170
Macromolecule	Uncharacterized protein (protein)
Unique Ligands	CA, FE

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6SV1 \| pdb_00006sv1	Download File View File

Crystal structure of Rhodospirillum rubrum Rru_A0973 E34A variant

Marles-Wright, J., He, D.

(2020) J Biological Chem 295: 15511-15526

Released	2020-09-23
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Rhodospirillum rubrum
Macromolecule	Encapsulated Ferritin (protein)
Unique Ligands	CA, FE

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7ODW \| pdb_00007odw	Download File View File

Model of Haliangium ochraceum encapsulin from icosahedral single particle reconstruction

Marles-Wright, J., Basle, A., Clarke, D.J., Ross, J.

(2022) Sci Adv 8: eabj4461-eabj4461

Released	2022-03-09
Method	ELECTRON MICROSCOPY 2.5 Å
Organisms	Haliangium ochraceum DSM 14365
Macromolecule	Linocin_M18 bacteriocin protein (protein)

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7OE2 \| pdb_00007oe2	Download File View File

Model of closed pentamer of the Haliangium ochraceum encapsulin from symmetry expansion of icosahedral single particle reconstruction

Marles-Wright, J., Basle, A., Clarke, D.J., Ross, J.

(2022) Sci Adv 8: eabj4461-eabj4461

Released	2022-02-09
Method	ELECTRON MICROSCOPY 2.4 Å
Organisms	Haliangium ochraceum DSM 14365
Macromolecule	Haliangium ochraceum Encapsulated ferritin localisation sequence (protein) Linocin_M18 bacteriocin protein (protein)

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7OEU \| pdb_00007oeu	Download File View File

Model of open pentamer of the Haliangium ochraceum encapsulin from symmetry expansion of icosahedral single particle reconstruction

Marles-Wright, J., Basle, A., Clarke, D.J., Ross, J.

(2022) Sci Adv 8: eabj4461-eabj4461

Released	2022-02-09
Method	ELECTRON MICROSCOPY 2.64 Å
Organisms	Haliangium ochraceum DSM 14365
Macromolecule	Haliangium ochraceum encapsulated ferritin (protein) Linocin_M18 bacteriocin protein (protein)

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8DLE \| pdb_00008dle	Download File View File

Crosslinked Crystal Structure of the 8-amino-7-oxonanoate synthase, BioF, and Benzene Sulfonyl Fluoride-crypto Acyl Carrier Protein, BSF-ACP

Chen, A., Davis, T.D., Louie, G.V., Bowman, M.E., Noel, J.P., Burkart, M.D.

(2024) J Am Chem Soc 146: 1388-1395

Released	2023-07-12
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli
Macromolecule	8-amino-7-oxononanoate synthase (protein) Acyl carrier protein (protein)
Unique Ligands	EDO, PLP, SO4, SWC

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8RPC \| pdb_00008rpc	Download File View File

Crystal structure of PfCLK3 with TCMDC-135051

Yelland, T.S., Benazir, A., Hole, A.

(2024) J Med Chem 67: 18895-18910

Released	2024-11-06
Method	X-RAY DIFFRACTION 2.079 Å
Organisms	Plasmodium falciparum
Macromolecule	non-specific serine/threonine protein kinase (protein)
Unique Ligands	A1H19, EDO, GOL, SO4

1 to 25 of 25 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

Symmetry Type

SCOP Classification

2X8U | pdb_00002x8u

2XBN | pdb_00002xbn

3EFR | pdb_00003efr

3EFS | pdb_00003efs

3FJP | pdb_00003fjp

4BMK | pdb_00004bmk

4C3S | pdb_00004c3s

4TQX | pdb_00004tqx

5DA5 | pdb_00005da5

5DBV | pdb_00005dbv

5DRU | pdb_00005dru

5K1R | pdb_00005k1r

5L89 | pdb_00005l89

5L8B | pdb_00005l8b

5L8F | pdb_00005l8f

5L8G | pdb_00005l8g

5N5E | pdb_00005n5e

5N5F | pdb_00005n5f

6SUW | pdb_00006suw

6SV1 | pdb_00006sv1

7ODW | pdb_00007odw

7OE2 | pdb_00007oe2

7OEU | pdb_00007oeu

8DLE | pdb_00008dle

8RPC | pdb_00008rpc