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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yu, P."

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Search Summary

This query matches 61 Structures.

Refinements

Structure Determination Methodology

experimental (61)

Scientific Name of Source Organism

	Homo sapiens (29)
	Severe acute respiratory syndrome coronavirus 2 (7)
	Vibrio vulnificus (7)
	Caldanaerobacter subterraneus subsp. tengcongensis (5)
	Thermus thermophilus (5)
	Escherichia phage RB69 (2)
	Fusobacterium nucleatum (2)
	Tequatrovirus T4 (2)
	Bordetella bronchiseptica RB50 (1)
	Escherichia coli (1)

More...

Taxonomy

	Eukaryota (30)
	Bacteria (24)
	Riboviria (8)
	Duplodnaviria (4)

Experimental Method

	X-RAY DIFFRACTION (38)
	SOLUTION NMR (15)
	ELECTRON MICROSCOPY (8)
	SOLUTION SCATTERING (4)

Polymer Entity Type

	Protein (42)
	RNA (19)
	DNA (1)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (13)
	2.5 - 3.0 (12)
	3.0 - 3.5 (12)
	3.5 - 4.0 (4)
	> 4.5 (1)

Release Date

	1995 - 1999 (4)
	2000 - 2004 (4)
	2005 - 2009 (10)
	2010 - 2014 (13)
	2015 - 2019 (7)
	2020 - 2024 (23)

Enzyme Classification Name

	Transferases (16)
	Hydrolases (5)
	Isomerases (1)

Membrane Protein Annotation

	OPM (3)
	PDBTM (3)
	MemProtMD (2)
	mpstruc (1)

Symmetry Type

	Asymmetric (35)
	Cyclic (7)

SCOP Classification

	Alpha and beta proteins (a+b) (17)
	All beta proteins (5)
	All alpha proteins (9)
	Alpha and beta proteins (a/b) (5)
	Multi-domain proteins (alpha and beta) (2)
	Artifacts (1)

AllSelected

1 to 25 of 61 Structures

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1NOY \| pdb_00001noy	Download File View File

DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX

Wang, J., Yu, P., Lin, T.C., Konigsberg, W.H., Steitz, T.A.

(1996) Biochemistry 35: 8110-8119

Released	1996-10-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Tequatrovirus T4
Macromolecule	PROTEIN (DNA POLYMERASE (E.C.2.7.7.7)) (protein) DNA (5'-D(TPTP*T)-3') (nucleic acid)
Unique Ligands	MN, ZN

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1NOZ \| pdb_00001noz	Download File View File

T4 DNA POLYMERASE FRAGMENT (RESIDUES 1-388) AT 110K

Wang, J., Yu, P., Lin, T.C., Konigsberg, W.H., Steitz, T.A.

(1996) Biochemistry 35: 8110-8119

Released	1996-10-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Tequatrovirus T4
Macromolecule	DNA POLYMERASE (protein)

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1OP1 \| pdb_00001op1	Download File View File

Solution NMR structure of domain 1 of receptor associated protein

Wu, Y., Migliorini, M., Yu, P., Strickland, D.K., Wang, Y.-X.

(2003) J Biomol NMR 26: 187-188

Released	2003-08-26
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Alpha-2-macroglobulin receptor-associated protein precursor (protein)

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1OV2 \| pdb_00001ov2	Download File View File

Ensemble of the solution structures of domain one of receptor associated protein

Wu, Y., Migliorini, M., Yu, P., Strickland, D.K., Wang, Y.X.

(2003) J Biomol NMR 26: 187-188

Released	2004-04-06
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Alpha-2-macroglobulin receptor-associated protein precursor (protein)

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1S2F \| pdb_00001s2f	Download File View File

Average solution structure of a pseudo-5'-splice site from the negative regulator of splicing of Rous Sarcoma virus

Cabello-Villegas, J., Giles, K.E., Soto, A.M., Yu, P., Beemon, K.L., Wang, Y.X.

(2004) RNA 10: 1388-1398

Released	2004-08-31
Method	SOLUTION NMR
Macromolecule	5'-R(GPGPGPGPAPGPUPGPGPUPUPUPGPUPAPUPCPCPUPUPCPCP*C)-3' (nucleic acid)

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1S34 \| pdb_00001s34	Download File View File

Solution structure of residues 907-929 from Rous Sarcoma Virus

Cabello-Villegas, J., Giles, K.E., Soto, A.M., Yu, P., Beemon, K.L., Wang, Y.X.

(2004) RNA 10: 1388-1398

Released	2004-08-31
Method	SOLUTION NMR
Macromolecule	5'-R(GPGPGPGPAPGPUPGPGPUPUPUPGPUPAPUPCPCPUPUPCPCP*C)-3' (nucleic acid)

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1WAF \| pdb_00001waf	Download File View File

DNA POLYMERASE FROM BACTERIOPHAGE RB69

Wang, J., Satter, A.K.M.A., Wang, C.C., Karam, J.D., Konigsberg, W.H., Steitz, T.A.

(1997) Cell 89: 1087-1099

Released	1998-01-14
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Escherichia phage RB69
Macromolecule	DNA POLYMERASE (protein)
Unique Ligands	GMP

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1WAJ \| pdb_00001waj	Download File View File

DNA POLYMERASE FROM BACTERIOPHAGE RB69

Wang, J., Satter, A.K.M.A., Wang, C.C., Karam, J.D., Konigsberg, W.H., Steitz, T.A.

(1997) Cell 89: 1087-1099

Released	1998-01-14
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia phage RB69
Macromolecule	DNA POLYMERASE (protein)
Unique Ligands	5GP

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2E34 \| pdb_00002e34	Download File View File

L11 structure with RDC and RG refinement

Lee, D., Walsh, J.D., Yu, P., Markus, M.A., Choli-Papadopoulous, T., Schwieters, C.D., Krueger, S., Draper, D.E., Wang, Y.X.

(2007) J Mol Biology 367: 1007-1022

Released	2007-06-19
Method	SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L11 (protein)

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2E35 \| pdb_00002e35	Download File View File

the minimized average structure of L11 with rg refinement

Lee, D., Walsh, J.D., Yu, P., Markus, M.A., Choli-Papadopoulous, T., Schwieters, C.D., Krueger, S., Draper, D.E., Wang, Y.X.

(2007) J Mol Biology 367: 1007-1022

Released	2007-06-19
Method	SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L11 (protein)

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2E36 \| pdb_00002e36	Download File View File

L11 with SANS refinement

Lee, D., Walsh, J.D., Yu, P., Markus, M.A., Choli-Papadopoulous, T., Schwieters, C.D., Krueger, S., Draper, D.E., Wang, Y.X.

(2007) J Mol Biology 367: 1007-1022

Released	2007-06-19
Method	SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L11 (protein)

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2FTU \| pdb_00002ftu	Download File View File

solution structure of domain 3 of RAP

Lee, D., Walsh, J.D., Wang, Y.-X.

(2006) Mol Cell 22: 423-430

Released	2006-05-09
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Alpha-2-macroglobulin receptor-associated protein, domain 3 (protein)

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2H8W \| pdb_00002h8w	Download File View File

Solution structure of ribosomal protein L11

Lee, D., Walsh, J.D., Yu, P., Choli-Papadopoulou, T., Krueger, S., Draper, D., Wang, Y.-X.

(2007) J Mol Biology 367: 1007-1022

Released	2007-02-06
Method	SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L11 (protein)

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2KLJ \| pdb_00002klj	Download File View File

Solution Structure of gammaD-Crystallin with RDC and SAXS

Wang, J., Zuo, X., Yu, P., Byeon, I., Jung, J., Gronenborn, A.M., Wang, Y.

(2009) J Am Chem Soc 131: 10507-10515

Released	2009-10-06
Method	SOLUTION SCATTERING SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Gamma-crystallin D (protein)

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2KLK \| pdb_00002klk	Download File View File

Solution structure of GB1 A34F mutant with RDC and SAXS

Wang, J., Zuo, X., Yu, P., Byeon, I.L., Jung, J., Schwieters, C.D., Gronenborn, A.M., Wang, Y.

(2009) J Am Chem Soc 131: 10507-10515

Released	2009-10-06
Method	SOLUTION SCATTERING SOLUTION NMR
Organisms	Staphylococcus aureus
Macromolecule	IMMUNOGLOBULIN G-BINDING PROTEIN G (protein)

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2KLM \| pdb_00002klm	Download File View File

Solution Structure of L11 with SAXS and RDC

Wang, J., Zuo, X., Yu, P., Schwieters, C.D., Wang, Y.

(2009) J Am Chem Soc 131: 10507-10515

Released	2009-10-06
Method	SOLUTION SCATTERING SOLUTION NMR
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L11 (protein)

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2KRL \| pdb_00002krl	Download File View File

The ensemble of the solution global structures of the 102-nt ribosome binding structure element of the turnip crinkle virus 3' UTR RNA

Zuo, X., Wang, J., Yu, P., Eyler, D., Xu, H., Starich, M., Tiede, D., Simon, A., Kasprzak, W., Schwieters, C., Shapiro, B.

(2010) Proc Natl Acad Sci U S A 107: 1385-1390

Released	2011-02-09
Method	SOLUTION NMR SOLUTION SCATTERING
Organisms	Turnip crinkle virus
Macromolecule	RNA (102-MER) (nucleic acid)

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2P01 \| pdb_00002p01	Download File View File

The structure of receptor-associated protein(RAP)

Lee, D., Walsh, J.D., Migliorini, M., Yu, P., Cai, T., Schwieters, C.D., Krueger, S., Strickland, D.K., Wang, Y.X.

(2007) Protein Sci 16: 1628-1640

Released	2007-08-21
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Alpha-2-macroglobulin receptor-associated protein (protein)

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2P03 \| pdb_00002p03	Download File View File

The structure of receptor-associated protein(RAP)

Lee, D., Walsh, J.D., Migliorini, M., Yu, P., Cai, T., Schwieters, C.D., Krueger, S., Strickland, D.K., Wang, Y.X.

(2007) Protein Sci 16: 1628-1640

Released	2007-08-21
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Alpha-2-macroglobulin receptor-associated protein (protein)

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3LQ8 \| pdb_00003lq8	Download File View File

Structure of the kinase domain of c-Met bound to XL880 (GSK1363089)

Lougheed, J.C., Stout, T.J.

(2009) Cancer Res 69: 8009-8016

Released	2010-05-19
Method	X-RAY DIFFRACTION 2.02 Å
Organisms	Homo sapiens
Macromolecule	Hepatocyte growth factor receptor (protein)
Unique Ligands	88Z

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4ALU \| pdb_00004alu	Download File View File

Benzofuropyrimidinone Inhibitors of Pim-1

Stout, T.J., Adams, L.

(2012) Bioorg Med Chem Lett 22: 3732

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE PIM-1 (protein)
Unique Ligands	79O, IMD

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4ALV \| pdb_00004alv	Download File View File

Benzofuropyrimidinone Inhibitors of Pim-1

Stout, T.J., Adams, L.

(2012) Bioorg Med Chem Lett 22: 3732

Released	2013-01-16
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Homo sapiens
Macromolecule	SERINE/THREONINE-PROTEIN KINASE PIM-1 (protein)
Unique Ligands	IMD, R9P

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4ALW \| pdb_00004alw	Download File View File

Benzofuropyrimidinone Inhibitors of Pim-1

Stout, T.J., Adams, L.

(2012) Bioorg Med Chem Lett 22: 3732

Released	2013-01-16
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Homo sapiens
Macromolecule	PIM-1 KINASE (protein)
Unique Ligands	HY7, IMD

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4AN2 \| pdb_00004an2	Download File View File

Crystal structures of human MEK1 with carboxamide-based allosteric inhibitor XL518 (GDC-0973), or related analogs.

Rice, K.D., Aay, N., Anand, N.K., Blazey, C.M., Bowles, O.J., Bussenius, J., Costanzo, S., Curtis, J.K., Defina, S.C., Dubenko, L., Engst, S., Joshi, A.A., Kennedy, A.R., Kim, A.I., Koltun, E.S., Lougheed, J.C., Manalo, J.C.L., Martini, J.F., Nuss, J.M., Peto, C.J., Tsang, T.H., Yu, P., Johnston, S.

(2012) ACS Med Chem Lett 3: 416

Released	2012-12-19
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (protein)
Unique Ligands	ACP, EUI, MG

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4AN3 \| pdb_00004an3	Download File View File

Crystal structures of human MEK1 with carboxamide-based allosteric inhibitor XL518 (GDC-0973), or related analogs.

(2012) ACS Med Chem Lett 3: 416

Released	2012-12-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 (protein)
Unique Ligands	5Y0, ATP, MG

1 to 25 of 61 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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1NOY | pdb_00001noy

1NOZ | pdb_00001noz

1OP1 | pdb_00001op1

1OV2 | pdb_00001ov2

1S2F | pdb_00001s2f

1S34 | pdb_00001s34

1WAF | pdb_00001waf

1WAJ | pdb_00001waj

2E34 | pdb_00002e34

2E35 | pdb_00002e35

2E36 | pdb_00002e36

2FTU | pdb_00002ftu

2H8W | pdb_00002h8w

2KLJ | pdb_00002klj

2KLK | pdb_00002klk

2KLM | pdb_00002klm

2KRL | pdb_00002krl

2P01 | pdb_00002p01

2P03 | pdb_00002p03

3LQ8 | pdb_00003lq8

4ALU | pdb_00004alu

4ALV | pdb_00004alv

4ALW | pdb_00004alw

4AN2 | pdb_00004an2

4AN3 | pdb_00004an3