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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Li, S."

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Search Summary

This query matches 37 Structures.

Refinements

Structure Determination Methodology

experimental (37)

Scientific Name of Source Organism

	Escherichia coli (10)
	Bos taurus (4)
	Escherichia coli K-12 (4)
	Homo sapiens (4)
	Mus musculus (4)
	Aquifex aeolicus (3)
	Human herpesvirus 4 strain B95-8 (3)
	Norwalk virus (3)
	Equus caballus (2)
	Hepacivirus hominis (2)

More...

Taxonomy

	Eukaryota (17)
	Bacteria (14)
	Riboviria (6)
	Duplodnaviria (5)
	Monodnaviria (1)

Experimental Method

X-RAY DIFFRACTION (37)

Polymer Entity Type

	Protein (36)
	RNA (3)
	DNA (1)

Refinement Resolution (Å)

	1.5 - 2.0 (5)
	2.0 - 2.5 (17)
	2.5 - 3.0 (8)
	3.0 - 3.5 (6)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (14)
	2010 - 2014 (11)
	2015 - 2019 (1)
	2020 - 2024 (9)

Enzyme Classification Name

	Ligases (6)
	Transferases (14)
	Hydrolases (2)
	Oxidoreductases (1)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (20)
	Cyclic (8)
	Dihedral (8)
	Octahedral (2)
	Icosahedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (12)
	Artifacts (4)
	All alpha proteins (2)
	All beta proteins (2)

AllSelected

1 to 25 of 37 Structures

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1LP3 \| pdb_00001lp3	Download File View File

The Atomic Structure of Adeno-Associated Virus (AAV-2), a Vector for Human Gene Therapy

Xie, Q., Bu, W., Bhatia, S., Hare, J., Somasundaram, T., Azzi, A., Chapman, M.S.

(2002) Proc Natl Acad Sci U S A 99: 10405-10410

Released	2002-08-07
Method	X-RAY DIFFRACTION 3 Å
Organisms	adeno-associated virus 2
Macromolecule	AAV-2 capsid protein (protein)

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1LU5 \| pdb_00001lu5	Download File View File

2.4 Angstrom Crystal Structure of the Asymmetric Platinum Complex {Pt(ammine)(cyclohexylamine)}2+ Bound to a Dodecamer DNA Duplex

Silverman, A.P., Bu, W., Cohen, S.M., Lippard, S.J.

(2002) J Biological Chem 277: 49743-49749

Released	2002-12-20
Method	X-RAY DIFFRACTION 2.4 Å
Macromolecule	5'-D(CPCPTPCPTPGPGPTPCPTPCPC)-3' (nucleic acid) 5'-D(GPGPAPGPAPCPCPAPGPAPGPG)-3' (nucleic acid)
Unique Ligands	LPT

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1TGV \| pdb_00001tgv	Download File View File

Structure of E. coli Uridine Phosphorylase complexed with 5-Fluorouridine and sulfate

Bu, W., Settembre, E.C., Sanders, J.M., Begley, T.P., Ealick, S.E.

(2004) To be published

Released	2005-06-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	uridine phosphorylase (protein)
Unique Ligands	5UD, K, SO4

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1TGY \| pdb_00001tgy	Download File View File

Structure of E. coli Uridine Phosphorylase complexed with uracil and ribose 1-phosphate

Bu, W., Settembre, E.C., Sanders, J.M., Begley, T.P., Ealick, S.E.

(2004) To be published

Released	2005-06-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	uridine phosphorylase (protein)
Unique Ligands	K, R1P, URA

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1U1C \| pdb_00001u1c	Download File View File

Structure of E. coli uridine phosphorylase complexed to 5-benzylacyclouridine (BAU)

Bu, W., Settembre, E.C., Ealick, S.E.

(2005) Acta Crystallogr D Biol Crystallogr 61: 863-872

Released	2005-07-05
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	BAU, K, PO4

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1U1D \| pdb_00001u1d	Download File View File

Structure of e. coli uridine phosphorylase complexed to 5-(phenylthio)acyclouridine (ptau)

Bu, W., Settembre, E.C., Ealick, S.E.

(2005) Acta Crystallogr D Biol Crystallogr 61: 863-872

Released	2005-07-05
Method	X-RAY DIFFRACTION 2.001 Å
Organisms	Escherichia coli
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	181, K, PO4

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1U1E \| pdb_00001u1e	Download File View File

Structure of e. coli uridine phosphorylase complexed to 5(phenylseleno)acyclouridine (PSAU)

Bu, W., Settembre, E.C., Ealick, S.E.

(2005) Acta Crystallogr D Biol Crystallogr 61: 863-872

Released	2005-07-05
Method	X-RAY DIFFRACTION 2.001 Å
Organisms	Escherichia coli
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	182, K, PO4

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1U1F \| pdb_00001u1f	Download File View File

Structure of e. coli uridine phosphorylase complexed to 5-(m-(benzyloxy)benzyl)acyclouridine (BBAU)

Bu, W., Settembre, E.C., Ealick, S.E.

(2005) Acta Crystallogr D Biol Crystallogr 61: 863-872

Released	2005-07-05
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	183, K, PO4

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1U1G \| pdb_00001u1g	Download File View File

Structure of E. coli uridine phosphorylase complexed to 5-(m-(benzyloxy)benzyl)barbituric acid (BBBA)

Bu, W., Settembre, E.C., Ealick, S.E.

(2005) Acta Crystallogr D Biol Crystallogr 61: 863-872

Released	2005-07-05
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Escherichia coli
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	BBB, K

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3BQJ \| pdb_00003bqj	Download File View File

VA387 polypeptide

Bu, W., Mamedova, A., Tan, M., Jiang, J., Hegde, R.

(2008) J Virol 82: 5340-5347

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Norovirus isolates
Macromolecule	va387 polypeptide (protein)

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3BY1 \| pdb_00003by1	Download File View File

Unliganded Norvalk Virus P domain

Hegde, R., Bu, W.

(2008) J Virol 82: 5340-5347

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.69 Å
Organisms	Norwalk virus
Macromolecule	58 kd capsid protein (protein)

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3BY2 \| pdb_00003by2	Download File View File

Norwalk P polypeptide (228-523)

Hegde, R., Bu, W.

(2008) J Virol 82: 5340-5347

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Norwalk virus
Macromolecule	58 kd capsid protein (protein)

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3D26 \| pdb_00003d26	Download File View File

Norwalk P domain A-trisaccharide complex

Hegde, R., Bu, W.

(2008) J Virol 82: 5340-5347

Released	2008-06-10
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Norwalk virus
Macromolecule	58 kd capsid protein (protein)
Unique branched monosaccharides	FUC, GAL, NGA

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3H0L \| pdb_00003h0l	Download File View File

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Soll, D., Smith, J.L.

(2009) J Mol Biology 391: 703-716

Released	2009-07-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aquifex aeolicus
Macromolecule	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (protein) Glutamyl-tRNA(Gln) amidotransferase subunit A (protein) Glutamyl-tRNA(Gln) amidotransferase subunit C (protein)
Unique Ligands	ADP, ASN, MG, ZN

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3H0M \| pdb_00003h0m	Download File View File

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Soll, D., Smith, J.L.

(2009) J Mol Biology 391: 703-716

Released	2009-07-21
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Aquifex aeolicus
Macromolecule	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (protein) Glutamyl-tRNA(Gln) amidotransferase subunit A (protein) Glutamyl-tRNA(Gln) amidotransferase subunit C (protein)
Unique Ligands	GLN, MG, ZN

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3H0R \| pdb_00003h0r	Download File View File

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Soll, D., Smith, J.L.

(2009) J Mol Biology 391: 703-716

Released	2009-07-21
Method	X-RAY DIFFRACTION 3 Å
Organisms	Aquifex aeolicus
Macromolecule	Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (protein) Glutamyl-tRNA(Gln) amidotransferase subunit A (protein) Glutamyl-tRNA(Gln) amidotransferase subunit C (protein)
Unique Ligands	ADP, ASN, ASP, ATP, MN, ZN

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3KU4 \| pdb_00003ku4	Download File View File

Trapping of an oxocarbenium ion intermediate in UP crystals

Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.

(2010) Biochemistry 49: 3499-3509

Released	2010-04-28
Method	X-RAY DIFFRACTION 2.099 Å
Organisms	Bos taurus
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	SO4

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3KUK \| pdb_00003kuk	Download File View File

Trapping of an oxocarbenium ion intermediate in UP crystals

Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.

(2010) Biochemistry 49: 3499-3509

Released	2010-04-28
Method	X-RAY DIFFRACTION 2.783 Å
Organisms	Bos taurus
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	DUR, SO4

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3KVR \| pdb_00003kvr	Download File View File

Trapping of an oxocarbenium ion intermediate in UP crystals

Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.

(2010) Biochemistry 49: 3499-3509

Released	2010-04-28
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bos taurus
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	R2G, SO4, URF

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3KVV \| pdb_00003kvv	Download File View File

Trapping of an oxocarbenium ion intermediate in UP crystals

Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.

(2010) Biochemistry 49: 3499-3509

Released	2010-04-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli K-12
Macromolecule	Uridine phosphorylase (protein)
Unique Ligands	R2B, SO4, URF

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3KVY \| pdb_00003kvy	Download File View File

Trapping of an oxocarbenium ion intermediate in UP crystals

Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.

(2010) Biochemistry 49: 3499-3509

Released	2010-04-28
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bos taurus
Macromolecule	Uridine Phosphorylase (protein)
Unique Ligands	R2B, SO4, URA

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3U90 \| pdb_00003u90	Download File View File

apoferritin: complex with SDS

Liu, R., Bu, W., Xi, J., Mortazavi, S.R., Cheung-Lau, J.C., Dmochowski, I.J., Loll, P.J.

(2012) Acta Crystallogr D Biol Crystallogr 68: 497-504

Released	2012-04-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, SDS

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3ZJT \| pdb_00003zjt	Download File View File

Ternary complex of E.coli leucyl-tRNA synthetase, tRNA(Leu)574 and the benzoxaborole AN3017 in the editing conformation

Cusack, S., Palencia, A., Crepin, T., Hernandez, V., Akama, T., Baker, S.J., Bu, W., Feng, L., Freund, Y.R., Liu, L., Meewan, M., Mohan, M., Mao, W., Rock, F.L., Sexton, H., Sheoran, A., Zhang, Y., Zhang, Y., Zhou, Y., Nieman, J.A., Anugula, M.R., Keramane, E.M., Savariraj, K., Reddy, D.S., Sharma, R., Subedi, R., Singh, R., OLeary, A., Simon, N.L., DeMarsh, P.L., Mushtaq, S., Warner, M., Livermore, D.M., Alley, M.R.K., Plattner, J.J.

(2013) Antimicrob Agents Chemother 57: 1394

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli Escherichia coli K-12
Macromolecule	LEUCYL-TRNA SYNTHETASE (protein) TRNALEU5 UAA ISOACCEPTOR (nucleic acid)
Unique Ligands	MG

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3ZJU \| pdb_00003zju	Download File View File

Ternary complex of E .coli leucyl-tRNA synthetase, tRNA(Leu) and the benzoxaborole AN3016 in the editing conformation

(2013) Antimicrob Agents Chemother 57: 1394

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli Escherichia coli K-12
Macromolecule	LEUCYL-TRNA SYNTHETASE (protein) TRNALEU5 UAA ISOACCEPTOR (nucleic acid)
Unique Ligands	MG

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3ZJV \| pdb_00003zjv	Download File View File

Ternary complex of E .coli leucyl-tRNA synthetase, tRNA(Leu) and the benzoxaborole AN3213 in the editing conformation

(2013) Antimicrob Agents Chemother 57: 1394

Released	2013-04-17
Method	X-RAY DIFFRACTION 2.31 Å
Organisms	Escherichia coli Escherichia coli K-12
Macromolecule	LEUCINE--TRNA LIGASE (protein) TRNALEU5 UAA ISOACCEPTOR (nucleic acid)

1 to 25 of 37 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

1LP3 | pdb_00001lp3

1LU5 | pdb_00001lu5

1TGV | pdb_00001tgv

1TGY | pdb_00001tgy

1U1C | pdb_00001u1c

1U1D | pdb_00001u1d

1U1E | pdb_00001u1e

1U1F | pdb_00001u1f

1U1G | pdb_00001u1g

3BQJ | pdb_00003bqj

3BY1 | pdb_00003by1

3BY2 | pdb_00003by2

3D26 | pdb_00003d26

3H0L | pdb_00003h0l

3H0M | pdb_00003h0m

3H0R | pdb_00003h0r

3KU4 | pdb_00003ku4

3KUK | pdb_00003kuk

3KVR | pdb_00003kvr

3KVV | pdb_00003kvv

3KVY | pdb_00003kvy

3U90 | pdb_00003u90

3ZJT | pdb_00003zjt

3ZJU | pdb_00003zju

3ZJV | pdb_00003zjv