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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Deng, P."

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Search Summary

This query matches 16 Structures.

Refinements

Structure Determination Methodology

experimental (16)

Scientific Name of Source Organism

	Homo sapiens (5)
	Bombyx mori (4)
	Xenopus laevis (4)
	Xenopus tropicalis (4)
	Arabidopsis thaliana (3)
	Amaranthus hypochondriacus (1)
	Cerebratulus lacteus (1)
	Streptococcus pyogenes (1)
	Streptococcus pyogenes serotype M1 (1)
	Thermothelomyces thermophilus ATCC 42464 (1)

More...

Taxonomy

	Eukaryota (15)
	Bacteria (1)
	other sequences (1)

Experimental Method

	ELECTRON MICROSCOPY (9)
	X-RAY DIFFRACTION (6)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (16)
	DNA (7)
	RNA (5)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.5 - 3.0 (4)
	3.0 - 3.5 (6)
	3.5 - 4.0 (3)
	> 4.5 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (1)
	2010 - 2014 (3)
	2015 - 2019 (2)
	2020 - 2024 (9)

Enzyme Classification Name

	Transferases (5)
	Hydrolases (4)

Symmetry Type

	Asymmetric (14)
	Cyclic (2)

SCOP Classification

	All alpha proteins (2)
	Alpha and beta proteins (a+b) (1)
	Membrane and cell surface proteins and peptides (1)
	Small proteins (1)

AllSelected

1 to 16 of 16 Structures

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1QFD \| pdb_00001qfd	Download File View File

NMR SOLUTION STRUCTURE OF ALPHA-AMYLASE INHIBITOR (AAI)

Lu, S., Deng, P., Liu, X., Luo, J., Han, R., Gu, X., Liang, S., Wang, X., Feng, L., Lozanov, V., Patthy, A., Pongor, S.

(1999) J Biological Chem 274: 20473-20478

Released	1999-07-16
Method	SOLUTION NMR
Organisms	Amaranthus hypochondriacus
Macromolecule	PROTEIN (ALPHA-AMYLASE INHIBITOR) (protein)

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1V07 \| pdb_00001v07	Download File View File

CRYSTAL STRUCTURE OF ThrE11Val mutant of THE NERVE TISSUE MINI-HEMOGLOBIN FROM THE NEMERTEAN WORM CEREBRATULUS LACTEUS

Pesce, A., Nardini, M., Ascenzi, P., Geuens, E., Dewilde, S., Moens, L., Bolognesi, M., Riggs, A., Hale, A., Deng, P., Nienhaus, G.U., Olson, J.S., Nienhaus, K.

(2004) J Biological Chem 279: 33662

Released	2004-06-03
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Cerebratulus lacteus
Macromolecule	NEURAL HEMOGLOBIN (protein)
Unique Ligands	HEM, OXY, SO4

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4LG5 \| pdb_00004lg5	Download File View File

ABA-mimicking ligand QUINABACTIN in complex with ABA receptor PYL2 and PP2C HAB1

Zhou, X.E., Gao, M., Liu, X., Zhang, Y., Xue, X., Melcher, K., Gao, P., Wang, F., Zeng, L., Zhao, Y., Zhao, Y., Deng, P., Zhong, D., Zhu, J.-K., Xu, Y., Xu, H.E.

(2013) Cell Res 23: 1043-1054

Released	2013-08-14
Method	X-RAY DIFFRACTION 2.88 Å
Organisms	Arabidopsis thaliana
Macromolecule	Abscisic acid receptor PYL2 (protein) Protein phosphatase 2C 16 (protein)
Unique Ligands	A1O, MG

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4LGA \| pdb_00004lga	Download File View File

ABA-mimicking ligand N-(2-OXO-1-PROPYL-1,2,3,4-TETRAHYDROQUINOLIN-6-YL)-1-PHENYLMETHANESULFONAMIDE in complex with ABA receptor PYL2 and PP2C HAB1

Zhou, X.E., Gao, M., Liu, X., Zhang, Y., Xue, X., Melcher, K., Gao, P., Wang, F., Zeng, L., Zhao, Y., Zhao, Y., Deng, P., Zhong, D., Zhu, J.-K., Xu, Y., Xu, H.E.

(2013) Cell Res 23: 1043-1054

Released	2013-08-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Arabidopsis thaliana
Macromolecule	Abscisic acid receptor PYL2 (protein) Protein phosphatase 2C 16 (protein)
Unique Ligands	A2O, MG, SO4

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4LGB \| pdb_00004lgb	Download File View File

ABA-mimicking ligand N-(1-METHYL-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-6-YL)-1-(4-METHYLPHENYL)METHANESULFONAMIDE in complex with ABA receptor PYL2 and PP2C HAB1

Zhou, X.E., Gao, M., Liu, X., Zhang, Y., Xue, X., Melcher, K., Gao, P., Wang, F., Zeng, L., Zhao, Y., Zhao, Y., Deng, P., Zhong, D., Zhu, J.-K., Xu, Y., Xu, H.E.

(2013) Cell Res 23: 1043-1054

Released	2013-08-14
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Arabidopsis thaliana
Macromolecule	Abscisic acid receptor PYL2 (protein) Protein phosphatase 2C 16 (protein)
Unique Ligands	1W7, MG, SO4

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4XEY \| pdb_00004xey	Download File View File

Crystal structure of an SH2-kinase domain construct of c-Abl tyrosine kinase

Lorenz, S., Deng, P., Kuriyan, J.

(2015) Biochem J 468: 283-291

Released	2015-04-01
Method	X-RAY DIFFRACTION 2.891 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase ABL1 (protein)
Unique Ligands	1N1

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6AF0 \| pdb_00006af0	Download File View File

Structure of Ctr9, Paf1 and Cdc73 ternary complex from Myceliophthora thermophila

Wang, Z., Deng, P., Zhou, Y.

(2018) Proc Natl Acad Sci U S A 115: 9998-10003

Released	2018-09-19
Method	X-RAY DIFFRACTION 2.88 Å
Organisms	Thermothelomyces thermophilus ATCC 42464
Macromolecule	Cdc73 protein (protein) Ctr9 protein (protein) Paf1 protein (protein)

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7CRO \| pdb_00007cro	Download File View File

NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP

Li, W., Tian, W., Yuan, G., Deng, P., Gozani, O., Patel, D., Wang, Z.

(2021) Nature 590: 498-503

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.75 Å
Organisms	Homo sapiens Xenopus laevis Xenopus tropicalis
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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7CRP \| pdb_00007crp	Download File View File

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)

Li, W., Tian, W., Yuan, G., Deng, P., Gozani, O., Patel, D., Wang, Z.

(2021) Nature 590: 498-503

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens Xenopus laevis Xenopus tropicalis
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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7CRQ \| pdb_00007crq	Download File View File

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)

Li, W., Tian, W., Yuan, G., Deng, P., Gozani, O., Patel, D., Wang, Z.

(2021) Nature 590: 498-503

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.15 Å
Organisms	Homo sapiens Xenopus laevis Xenopus tropicalis
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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7CRR \| pdb_00007crr	Download File View File

Native NSD3 bound to 187-bp nucleosome

Li, W., Tian, W., Yuan, G., Deng, P., Gozani, O., Patel, D., Wang, Z.

(2021) Nature 590: 498-503

Released	2020-10-21
Method	ELECTRON MICROSCOPY 3.48 Å
Organisms	Homo sapiens Xenopus laevis Xenopus tropicalis synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2
Unique Ligands	SAM, ZN

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7V59 \| pdb_00007v59	Download File View File

Cryo-EM structure of spyCas9-sgRNA-DNA dimer

Liu, J., Deng, P.

(2021) Chem Sci 12: 12776-12784

Released	2022-08-17
Method	ELECTRON MICROSCOPY 5.26 Å
Organisms	Streptococcus pyogenes Streptococcus pyogenes serotype M1
Macromolecule	CRISPR-associated endonuclease Cas9/Csn1 (protein) DNA (49-MER) (nucleic acid) RNA (115-MER) (nucleic acid)

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8IBW \| pdb_00008ibw	Download File View File

Structure of R2 with 3'UTR and DNA in binding state

Deng, P., Tan, S., Wang, J., Liu, J.J.

(2023) Cell 186: 2865-2879.e20

Released	2023-09-20
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Bombyx mori
Macromolecule	Reverse transcriptase-like protein (protein) 3'UTR (nucleic acid) DNA (60-MER) (nucleic acid)
Unique Ligands	ZN

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8IBX \| pdb_00008ibx	Download File View File

Structure of R2 with 3'UTR and DNA in unwinding state

Deng, P., Tan, S., Wang, J., Liu, J.J.

(2023) Cell 186: 2865-2879.e20

Released	2023-09-20
Method	ELECTRON MICROSCOPY 3.74 Å
Organisms	Bombyx mori
Macromolecule	Reverse transcriptase-like protein (protein) 3'UTR (nucleic acid) DNA (60-MER) (nucleic acid)
Unique Ligands	ZN

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8IBY \| pdb_00008iby	Download File View File

Structure of R2 with 5'ORF

Deng, P., Tan, S., Wang, J., Liu, J.J.

(2023) Cell 186: 2865-2879.e20

Released	2023-09-20
Method	ELECTRON MICROSCOPY 3.47 Å
Organisms	Bombyx mori
Macromolecule	Reverse transcriptase-like protein (protein) 5'ORF RNA (nucleic acid)
Unique Ligands	ZN

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8IBZ \| pdb_00008ibz	Download File View File

Structure of R2 with 5'ORF and 3'UTR

Deng, P., Tan, S., Wang, J., Liu, J.J.

(2023) Cell 186: 2865-2879.e20

Released	2023-09-20
Method	ELECTRON MICROSCOPY 3.04 Å
Organisms	Bombyx mori
Macromolecule	Reverse transcriptase-like protein (protein) 5ORF-linker-3UTR (nucleic acid)
Unique Ligands	ZN

1 to 16 of 16 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.

1QFD | pdb_00001qfd

NMR SOLUTION STRUCTURE OF ALPHA-AMYLASE INHIBITOR (AAI)

1V07 | pdb_00001v07

CRYSTAL STRUCTURE OF ThrE11Val mutant of THE NERVE TISSUE MINI-HEMOGLOBIN FROM THE NEMERTEAN WORM CEREBRATULUS LACTEUS

4LG5 | pdb_00004lg5

ABA-mimicking ligand QUINABACTIN in complex with ABA receptor PYL2 and PP2C HAB1

4LGA | pdb_00004lga

ABA-mimicking ligand N-(2-OXO-1-PROPYL-1,2,3,4-TETRAHYDROQUINOLIN-6-YL)-1-PHENYLMETHANESULFONAMIDE in complex with ABA receptor PYL2 and PP2C HAB1

4LGB | pdb_00004lgb

ABA-mimicking ligand N-(1-METHYL-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-6-YL)-1-(4-METHYLPHENYL)METHANESULFONAMIDE in complex with ABA receptor PYL2 and PP2C HAB1

4XEY | pdb_00004xey

Crystal structure of an SH2-kinase domain construct of c-Abl tyrosine kinase

6AF0 | pdb_00006af0

Structure of Ctr9, Paf1 and Cdc73 ternary complex from Myceliophthora thermophila

7CRO | pdb_00007cro

NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP

7CRP | pdb_00007crp

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)

7CRQ | pdb_00007crq

NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)

7CRR | pdb_00007crr

Native NSD3 bound to 187-bp nucleosome

7V59 | pdb_00007v59

Cryo-EM structure of spyCas9-sgRNA-DNA dimer

8IBW | pdb_00008ibw

Structure of R2 with 3'UTR and DNA in binding state

8IBX | pdb_00008ibx

Structure of R2 with 3'UTR and DNA in unwinding state

8IBY | pdb_00008iby

Structure of R2 with 5'ORF

8IBZ | pdb_00008ibz

Structure of R2 with 5'ORF and 3'UTR

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

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Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1QFD | pdb_00001qfd

1V07 | pdb_00001v07

4LG5 | pdb_00004lg5

4LGA | pdb_00004lga

4LGB | pdb_00004lgb

4XEY | pdb_00004xey

6AF0 | pdb_00006af0

7CRO | pdb_00007cro

7CRP | pdb_00007crp

7CRQ | pdb_00007crq

7CRR | pdb_00007crr

7V59 | pdb_00007v59

8IBW | pdb_00008ibw

8IBX | pdb_00008ibx

8IBY | pdb_00008iby

8IBZ | pdb_00008ibz