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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Petzold, G."

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Search Summary

This query matches 42 Structures.

Refinements

Structure Determination Methodology

experimental (42)

Scientific Name of Source Organism

	Homo sapiens (39)
	Bacillus subtilis (3)
	Rattus norvegicus (1)
	Saccharomyces cerevisiae (1)
	Saccharomyces cerevisiae S288C (1)

Taxonomy

	Eukaryota (39)
	Bacteria (3)

Experimental Method

	X-RAY DIFFRACTION (38)
	ELECTRON MICROSCOPY (2)
	SOLUTION NMR (2)

Polymer Entity Type

Protein (42)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (2)
	2.5 - 3.0 (1)
	3.0 - 3.5 (24)
	3.5 - 4.0 (8)
	4.0 - 4.5 (1)
	> 4.5 (3)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (4)
	2015 - 2019 (7)
	2020 - 2024 (29)

Enzyme Classification Name

	Transferases (32)
	Hydrolases (1)
	Ligases (1)

Symmetry Type

	Asymmetric (40)
	Cyclic (3)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (2)
	Artifacts (1)

AllSelected

1 to 25 of 42 Structures

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2M6N \| pdb_00002m6n	Download File View File

3D solution structure of EMI1 (Early Mitotic Inhibitor 1)

Frye, J.J., Brown, N.G., Petzold, G., Watson, E.R., Royappa, G.R., Nourse, A., Jarvis, M., Kriwacki, R.W., Peters, J., Stark, H., Schulman, B.A.

(2013) Nat Struct Mol Biol 20: 827-835

Released	2013-05-29
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	F-box only protein 5 (protein)
Unique Ligands	ZN

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2MT5 \| pdb_00002mt5	Download File View File

Isolated Ring domain

Brown, N.G., Watson, E.R., Weissman, F., Royappa, G., Schulman, B., Jarvis, M., Vanderlinden, R., Frye, J.J., Qiao, R., Petzold, G., Peters, J., Stark, H.

(2014) Mol Cell 56: 246-260

Released	2014-10-29
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Anaphase-promoting complex subunit 11 (protein)
Unique Ligands	ZN

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2PX0 \| pdb_00002px0	Download File View File

Crystal structure of FlhF complexed with GMPPNP/Mg(2+)

Bange, G., Wild, K., Sinning, I.

(2007) Proc Natl Acad Sci U S A 104: 13621-13625

Released	2007-09-25
Method	X-RAY DIFFRACTION 3 Å
Organisms	Bacillus subtilis
Macromolecule	Flagellar biosynthesis protein flhF (protein)
Unique Ligands	GNP, MG

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2PX3 \| pdb_00002px3	Download File View File

Crystal structure of FlhF complexed with GTP/Mg(2+)

Bange, G., Wild, K., Sinning, I.

(2007) Proc Natl Acad Sci U S A 104: 13621-13625

Released	2007-09-25
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Bacillus subtilis
Macromolecule	Flagellar biosynthesis protein flhF (protein)
Unique Ligands	GTP, MG

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3SYN \| pdb_00003syn	Download File View File

Crystal structure of FlhF in complex with its activator

Bange, G., Kuemmerer, N., Wild, K., Sinning, I.

(2011) Nat Struct Mol Biol 18: 1376-1380

Released	2011-11-09
Method	X-RAY DIFFRACTION 3.063 Å
Organisms	Bacillus subtilis
Macromolecule	ATP-binding protein YlxH (protein) Flagellar biosynthesis protein flhF (protein)
Unique Ligands	AF3, GDP, MG, SO4

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4R2Y \| pdb_00004r2y	Download File View File

Crystal structure of APC11 RING domain

Brown, N.G., Watson, E.R., Weissmann, F., Jarvis, M.A., Vanderlinden, R., Grace, C.R.R., Frye, J.J., Dube, P., Qiao, R., Petzold, G., Cho, S.E., Alsharif, O., Bao, J., Zheng, J., Nourse, A., Kurinov, I., Peters, J.M., Stark, H., Schulman, B.A.

(2014) Mol Cell 56: 246-260

Released	2014-10-29
Method	X-RAY DIFFRACTION 1.755 Å
Organisms	Homo sapiens
Macromolecule	Anaphase-promoting complex subunit 11 (protein)
Unique Ligands	ZN

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4WSN \| pdb_00004wsn	Download File View File

Crystal structure of the COP9 signalosome, a P1 crystal form

Bunker, R.D., Lingaraju, G.M., Thoma, N.H.

(2016) Nature 531: 598-603

Released	2015-12-23
Method	X-RAY DIFFRACTION 5.5 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 8
Unique Ligands	ZN

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5FQD \| pdb_00005fqd	Download File View File

Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase

Petzold, G., Fischer, E.S., Thoma, N.H.

(2016) Nature 532: 127

Released	2016-02-24
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Homo sapiens
Macromolecule	CASEIN KINASE I ISOFORM ALPHA (protein) DNA DAMAGE-BINDING PROTEIN 1 (protein) PROTEIN CEREBLON (protein)
Unique Ligands	LVY, ZN

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5JG6 \| pdb_00005jg6	Download File View File

APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C

Brown, N.G., Zhang, W., Yu, S., Miller, D.J., Sidhu, S.S., Schulman, B.A.

(2016) Cell 165: 1440-1453

Released	2016-06-15
Method	X-RAY DIFFRACTION 2.0013 Å
Organisms	Homo sapiens
Macromolecule	Anaphase-promoting complex subunit 11 (protein) Polyubiquitin-B (protein)
Unique Ligands	ZN

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5L9T \| pdb_00005l9t	Download File View File

Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density

Brown, N.G., VanderLinden, R., Dube, P., Haselbach, D., Peters, J.M., Stark, H., Schulman, B.A.

(2016) Cell 165: 1440-1453

Released	2016-10-26
Method	ELECTRON MICROSCOPY 6.4 Å
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 17

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5L9U \| pdb_00005l9u	Download File View File

Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with a cross linked Ubiquitin variant-substrate-UBE2C (UBCH10) complex representing key features of multiubiquitination

Brown, N.G., VanderLinden, R., Dube, P., Haselbach, D., Peters, J.M., Stark, H., Schulman, B.A.

(2016) Cell 165: 1440-1453

Released	2016-09-14
Method	ELECTRON MICROSCOPY 6.4 Å
Organisms	Homo sapiens Rattus norvegicus Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 17

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6H0F \| pdb_00006h0f	Download File View File

Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)

Petzold, G., Bunker, R.D., Thoma, N.H.

(2018) Science 362: eaat0572

Released	2018-11-07
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Homo sapiens
Macromolecule	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 (protein) DNA-binding protein Ikaros (protein) Protein cereblon (protein)
Unique Ligands	Y70, ZN

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6H0G \| pdb_00006h0g	Download File View File

Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4)

Bunker, R.D., Petzold, G., Thoma, N.H.

(2018) Science 362:

Released	2018-11-07
Method	X-RAY DIFFRACTION 4.25 Å
Organisms	Homo sapiens
Macromolecule	DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DDB1 (DNA damage binding protein 1),DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1 (protein) Protein cereblon (protein) Zinc finger protein 692 (protein)
Unique Ligands	Y70, ZN

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6TD3 \| pdb_00006td3	Download File View File

Structure of DDB1 bound to CR8-engaged CDK12-cyclinK

Bunker, R.D., Petzold, G., Kozicka, Z., Thoma, N.H.

(2020) Nature 585: 293-297

Released	2020-06-17
Method	X-RAY DIFFRACTION 3.46 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	RC8

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8BU1 \| pdb_00008bu1	Download File View File

Structure of DDB1 bound to DS17-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 2.98 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	GOL, RQL

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8BU2 \| pdb_00008bu2	Download File View File

Structure of DDB1 bound to DS18-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.13 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	RVQ, SO4

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8BU3 \| pdb_00008bu3	Download File View File

Structure of DDB1 bound to DS19-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.42 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	EDO, RSI, SO4

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8BU4 \| pdb_00008bu4	Download File View File

Structure of DDB1 bound to DS22-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Focht, V., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.09 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	RQL, SO4

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8BU5 \| pdb_00008bu5	Download File View File

Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.134 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	CIT, RMF, SO4

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8BU6 \| pdb_00008bu6	Download File View File

Structure of DDB1 bound to DS55-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Focht, V., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.45 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	RQE, SO4

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8BU7 \| pdb_00008bu7	Download File View File

Structure of DDB1 bound to 21195-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.245 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	EDO, RS5, SO4

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8BU9 \| pdb_00008bu9	Download File View File

Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Focht, V., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.51 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	RRC, SO4

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8BUA \| pdb_00008bua	Download File View File

Structure of DDB1 bound to 919278-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.193 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	CIT, RVH

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8BUB \| pdb_00008bub	Download File View File

Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.42 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	CIT, RNU

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8BUC \| pdb_00008buc	Download File View File

Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Focht, V., Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

Released	2023-09-13
Method	X-RAY DIFFRACTION 3.85 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein) DNA damage-binding protein 1 (protein)
Unique Ligands	CIT, RKO, SO4

1 to 25 of 42 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

2M6N | pdb_00002m6n

2MT5 | pdb_00002mt5

2PX0 | pdb_00002px0

2PX3 | pdb_00002px3

3SYN | pdb_00003syn

4R2Y | pdb_00004r2y

4WSN | pdb_00004wsn

5FQD | pdb_00005fqd

5JG6 | pdb_00005jg6

5L9T | pdb_00005l9t

5L9U | pdb_00005l9u

6H0F | pdb_00006h0f

6H0G | pdb_00006h0g

6TD3 | pdb_00006td3

8BU1 | pdb_00008bu1

8BU2 | pdb_00008bu2

8BU3 | pdb_00008bu3

8BU4 | pdb_00008bu4

8BU5 | pdb_00008bu5

8BU6 | pdb_00008bu6

8BU7 | pdb_00008bu7

8BU9 | pdb_00008bu9

8BUA | pdb_00008bua

8BUB | pdb_00008bub

8BUC | pdb_00008buc