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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nicholls, R.A."

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Search Summary

This query matches 22 Structures.

Refinements

Structure Determination Methodology

experimental (22)

Scientific Name of Source Organism

	Helicobacter pylori 26695 (8)
	Homo sapiens (7)
	Escherichia coli K-12 (3)
	Arabidopsis thaliana (1)
	DNA molecule (1)
	Plasmodium berghei ANKA (1)
	Staphylococcus aureus (1)
	Streptomyces avermitilis MA-4680 = NBRC 14893 (1)

Taxonomy

	Bacteria (13)
	Eukaryota (9)
	unclassified sequences (1)

Experimental Method

X-RAY DIFFRACTION (22)

Polymer Entity Type

	Protein (22)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (10)
	2.5 - 3.0 (2)
	3.0 - 3.5 (1)
	> 4.5 (3)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (7)
	2015 - 2019 (3)
	2020 - 2024 (10)
	2025 - 2029 (1)

Enzyme Classification Name

	Lyases (7)
	Isomerases (8)
	Ligases (9)
	Translocases (1)

Symmetry Type

	Cyclic (20)
	Asymmetric (3)

SCOP Classification

All alpha proteins (1)

AllSelected

1 to 22 of 22 Structures

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Explore in 3D

2QMO \| pdb_00002qmo	Download File View File

Crystal structure of dethiobiotin synthetase (bioD) from Helicobacter pylori

Chruszcz, M., Xu, X., Cuff, M., Cymborowski, M., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2012) FEBS J 279: 1093-1105

Released	2007-07-31
Method	X-RAY DIFFRACTION 1.47 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Dethiobiotin synthetase (protein)
Unique Ligands	CL

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3MLE \| pdb_00003mle	Download File View File

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP

Nicholls, R., Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Joachimiak, A., Murshudov, G., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2012) FEBS J 279: 1093-1105

Released	2010-05-19
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Dethiobiotin synthetase (protein)
Unique Ligands	8AC, ADP, CL, MG, NO3, PO4

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3QXC \| pdb_00003qxc	Download File View File

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ATP

Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2012) FEBS J 279: 1093-1105

Released	2011-03-30
Method	X-RAY DIFFRACTION 1.34 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Dethiobiotin synthetase (protein)
Unique Ligands	ATP, EDO, GOL, MG, NO3, PEG

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3QXH \| pdb_00003qxh	Download File View File

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ADP and 8-aminocaprylic acid

Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Minor, C., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2012) FEBS J 279: 1093-1105

Released	2011-03-30
Method	X-RAY DIFFRACTION 1.36 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Dethiobiotin synthetase (protein)
Unique Ligands	8AC, ADP, EDO, MG, PO4

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3QXJ \| pdb_00003qxj	Download File View File

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP

Klimecka, M.M., Porebski, P.J., Chruszcz, M., Murzyn, K., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2012) FEBS J 279: 1093-1105

Released	2011-03-30
Method	X-RAY DIFFRACTION 1.38 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Dethiobiotin synthetase (protein)
Unique Ligands	EDO, GTP, MG, NO3

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3QXS \| pdb_00003qxs	Download File View File

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP

Klimecka, M.M., Porebski, P.J., Chruszcz, M., Jablonska, K., Murzyn, K., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2012) FEBS J 279: 1093-1105

Released	2011-03-30
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Dethiobiotin synthetase (protein)
Unique Ligands	ANP, EDO, MG, NO3

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3QXX \| pdb_00003qxx	Download File View File

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP and 8-aminocaprylic acid

Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2012) FEBS J 279: 1093-1105

Released	2011-03-30
Method	X-RAY DIFFRACTION 1.36 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Dethiobiotin synthetase (protein)
Unique Ligands	8AC, EDO, GDP, GOL, MG, PO4

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3QY0 \| pdb_00003qy0	Download File View File

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP

Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

(2012) FEBS J 279: 1093-1105

Released	2011-03-30
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Dethiobiotin synthetase (protein)
Unique Ligands	EDO, GDP, MG, PO4

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5AKB \| pdb_00005akb	Download File View File

MutS in complex with the N-terminal domain of MutL - crystal form 1

Groothuizen, F.S., Winkler, I., Cristovao, M., Fish, A., Winterwerp, H.H.K., Reumer, A., Marx, A.D., Hermans, N., Nicholls, R.A., Murshudov, G.N., Lebbink, J.H.G., Friedhoff, P., Sixma, T.K.

(2015) Elife 4: e06744-e06744

Released	2015-07-22
Method	X-RAY DIFFRACTION 4.71 Å
Organisms	Escherichia coli K-12
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTL (protein) DNA MISMATCH REPAIR PROTEIN MUTS (protein)
Unique Ligands	ANP

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5AKC \| pdb_00005akc	Download File View File

MutS in complex with the N-terminal domain of MutL - crystal form 2

Groothuizen, F.S., Winkler, I., Cristovao, M., Fish, A., Winterwerp, H.H.K., Reumer, A., Marx, A.D., Hermans, N., Nicholls, R.A., Murshudov, G.N., Lebbink, J.H.G., Friedhoff, P., Sixma, T.K.

(2015) Elife 4: e06744-e06744

Released	2015-07-22
Method	X-RAY DIFFRACTION 6.6 Å
Organisms	Escherichia coli K-12
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTL (protein) DNA MISMATCH REPAIR PROTEIN MUTS (protein)
Unique Ligands	ANP

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5AKD \| pdb_00005akd	Download File View File

MutS in complex with the N-terminal domain of MutL - crystal form 3

Groothuizen, F.S., Winkler, I., Cristovao, M., Fish, A., Winterwerp, H.H.K., Reumer, A., Marx, A.D., Hermans, N., Nicholls, R.A., Murshudov, G.N., Lebbink, J.H.G., Friedhoff, P., Sixma, T.K.

(2015) Elife 4: e06744-e06744

Released	2015-07-22
Method	X-RAY DIFFRACTION 7.6 Å
Organisms	Escherichia coli K-12
Macromolecule	DNA MISMATCH REPAIR PROTEIN MUTL (protein) DNA MISMATCH REPAIR PROTEIN MUTS (protein)
Unique Ligands	ANP

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6L69 \| pdb_00006l69	Download File View File

Crystal structure of CYP154C2 from Streptomyces avermitilis

Xu, L.H., Fushinobu, S.

(2020) Biochem Biophys Res Commun 522: 355-361

Released	2020-09-23
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Streptomyces avermitilis MA-4680 = NBRC 14893
Macromolecule	Cytochrome P450 hydroxylase (protein)
Unique Ligands	HEM

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6ZSP \| pdb_00006zsp	Download File View File

Human serine racemase bound to ATP and malonate.

Koulouris, C.R., Bax, B.D., Roe, S.M., Atack, J.R.

(2022) Commun Biol 5: 346-346

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Serine racemase (protein)
Unique Ligands	ATP, EDO, GOL, IMD, MG, MLI

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6ZUJ \| pdb_00006zuj	Download File View File

Human serine racemase holoenzyme from 20% DMSO soak (XChem crystallographic fragment screen).

Koulouris, C.R., Bax, B.D., Roe, S.M., Atack, J.R.

(2022) Commun Biol 5: 346-346

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Serine racemase (protein)
Unique Ligands	CA, DMS, EDO, GOL, MG, NA, PGE

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7NBC \| pdb_00007nbc	Download File View File

Crystal structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen.

Koulouris, C.R., Roe, S.M.

(2022) Commun Biol 5: 346-346

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.71 Å
Organisms	Homo sapiens
Macromolecule	Serine racemase (protein)
Unique Ligands	BP4, CA, EDO, GOL, MG, NA, PG0, PLP

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7NBD \| pdb_00007nbd	Download File View File

Crystal structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen.

Koulouris, C.R., Roe, S.M.

(2022) Commun Biol 5: 346-346

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.865 Å
Organisms	Homo sapiens
Macromolecule	Serine racemase (protein)
Unique Ligands	CA, EDO, GOL, JFS, MG, NA, PGE, PLP

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7NBF \| pdb_00007nbf	Download File View File

Crystal structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen.

Koulouris, C.R., Roe, S.M.

(2022) Commun Biol 5: 346-346

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Serine racemase (protein)
Unique Ligands	CA, CL, DMS, EDO, GOL, MG, NA, PGE, PLP, T6J

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7NBG \| pdb_00007nbg	Download File View File

Crystal structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen.

Koulouris, C.R., Roe, S.M.

(2022) Commun Biol 5: 346-346

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.53 Å
Organisms	Homo sapiens
Macromolecule	Serine racemase (protein)
Unique Ligands	CA, EDO, GOL, MG, NA, OXE, PG0, PGE, PLP, U78

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7NBH \| pdb_00007nbh	Download File View File

Crystal structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen.

Koulouris, C.R., Roe, S.M.

(2022) Commun Biol 5: 346-346

Released	2021-03-03
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Homo sapiens
Macromolecule	Serine racemase (protein)
Unique Ligands	CA, CL, EDO, GOL, MG, NA, PGE, W0D

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8BHD \| pdb_00008bhd	Download File View File

N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (Tbxo4 derivative crystal structure)

Benas, P., Jaramillo Ponce, J.R., Legrand, P., Frugier, M., Sauter, C.

(2023) Protein Sci 32: e4564-e4564

Released	2023-01-25
Method	X-RAY DIFFRACTION 3.17 Å
Organisms	Plasmodium berghei ANKA
Macromolecule	Glutamate--tRNA ligase (protein)
Unique Ligands	GOL, SO4, TB

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8RNZ \| pdb_00008rnz	Download File View File

Metal-binding domain 3 of copper-transporting ATPase RAN1 from Arabidopsis thaliana

Minges, A., Dluhosch, D., Groth, G.

(2025) To be published

Released	2025-01-29
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Arabidopsis thaliana
Macromolecule	Copper-transporting ATPase RAN1 (protein)

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9FZ6 \| pdb_00009fz6	Download File View File

A 2.58A crystal structure of S. aureus DNA gyrase and DNA with metals identified through anomalous scattering

Morgan, H., Duman, R., Bax, B.D., Warren, A.J.

(2024) Int J Mol Sci 25:

Released	2024-10-23
Method	X-RAY DIFFRACTION 2.58 Å
Organisms	DNA molecule Staphylococcus aureus
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA (5'-D(APGPCPCPGPTPAPG)-3') (nucleic acid) DNA (5'-D(APGPTPAPCPCPTPAPCPGPGPCP*T)-3') (nucleic acid)
Unique Ligands	BTB, GOL, MN

1 to 22 of 22 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

2QMO | pdb_00002qmo

3MLE | pdb_00003mle

3QXC | pdb_00003qxc

3QXH | pdb_00003qxh

3QXJ | pdb_00003qxj

3QXS | pdb_00003qxs

3QXX | pdb_00003qxx

3QY0 | pdb_00003qy0

5AKB | pdb_00005akb

5AKC | pdb_00005akc

5AKD | pdb_00005akd

6L69 | pdb_00006l69

6ZSP | pdb_00006zsp

6ZUJ | pdb_00006zuj

7NBC | pdb_00007nbc

7NBD | pdb_00007nbd

7NBF | pdb_00007nbf

7NBG | pdb_00007nbg

7NBH | pdb_00007nbh

8BHD | pdb_00008bhd

8RNZ | pdb_00008rnz

9FZ6 | pdb_00009fz6