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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Shen, B.W."

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Search Summary

This query matches 44 Structures.

Refinements

Structure Determination Methodology

experimental (44)

Scientific Name of Source Organism

	synthetic construct (15)
	Homo sapiens (9)
	Brevibacillus brevis (4)
	Sordaria macrospora k-hell (4)
	Geobacillus stearothermophilus (3)
	Staphylococcus warneri (3)
	Acinetobacter sp. NEB 394 (2)
	Aquipseudomonas alcaligenes (2)
	Deinococcus wulumuqiensis (2)
	Pseudomonas fluorescens (2)

More...

Taxonomy

	Bacteria (22)
	other sequences (15)
	Eukaryota (14)
	unclassified sequences (2)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (36)
	ELECTRON MICROSCOPY (8)

Polymer Entity Type

	Protein (44)
	DNA (13)

Refinement Resolution (Å)

	1.5 - 2.0 (8)
	2.0 - 2.5 (13)
	2.5 - 3.0 (12)
	3.0 - 3.5 (6)
	3.5 - 4.0 (4)
	> 4.5 (1)

Release Date

	1995 - 1999 (5)
	2000 - 2004 (3)
	2005 - 2009 (3)
	2010 - 2014 (4)
	2015 - 2019 (21)
	2020 - 2024 (8)

Enzyme Classification Name

	Transferases (9)
	Hydrolases (5)
	Oxidoreductases (1)

Membrane Protein Annotation

OPM (2)

Symmetry Type

	Asymmetric (26)
	Cyclic (16)
	Dihedral (4)

SCOP Classification

	Alpha and beta proteins (a/b) (4)
	Alpha and beta proteins (a+b) (3)
	All beta proteins (1)

AllSelected

1 to 25 of 44 Structures

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1B0A \| pdb_00001b0a	Download File View File

5,10, METHYLENE-TETRAHYDROPHOLATE DEHYDROGENASE/CYCLOHYDROLASE FROM E COLI.

Shen, B.W., Dyer, D., Huang, J.-Y., D'Ari, L., Rabinowitz, J., Stoddard, B.L.

(1999) Protein Sci 8: 1342-1349

Released	1999-06-29
Method	X-RAY DIFFRACTION 2.56 Å
Organisms	Escherichia coli K-12
Macromolecule	PROTEIN (FOLD BIFUNCTIONAL PROTEIN) (protein)

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1D7P \| pdb_00001d7p	Download File View File

Crystal structure of the c2 domain of human factor viii at 1.5 a resolution at 1.5 A

Pratt, K.P., Shen, B.W., Stoddard, B.L.

(1999) Nature 402: 439-442

Released	1999-12-01
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	COAGULATION FACTOR VIII PRECURSOR (protein)
Unique Ligands	CYS, GOL, SO4

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1GBN \| pdb_00001gbn	Download File View File

HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE

Shah, S.A., Shen, B.W., Brunger, A.T.

(1997) Structure 5: 1067-1075

Released	1998-06-03
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	ORNITHINE AMINOTRANSFERASE (protein)
Unique Ligands	GAB, GBC, PLP

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1OAT \| pdb_00001oat	Download File View File

ORNITHINE AMINOTRANSFERASE

Shen, B.W., Schirmer, T., Jansonius, J.N.

(1998) J Mol Biology 277: 81-102

Released	1998-04-01
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	ORNITHINE AMINOTRANSFERASE (protein)
Unique Ligands	PLP

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1Q33 \| pdb_00001q33	Download File View File

Crystal structure of human ADP-ribose pyrophosphatase NUDT9

Shen, B.W., Perraud, A.L., Scharenberg, A., Stoddard, B.L.

(2003) J Mol Biology 332: 385-398

Released	2003-09-30
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	BGC, SO4

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1QVJ \| pdb_00001qvj	Download File View File

structure of NUDT9 complexed with ribose-5-phosphate

Shen, B.W., Perraud, A.-L., Scharenberg, A.S., Stoddard, B.L.

(2003) J Mol Biology 332: 385-398

Released	2003-09-16
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribose pyrophosphatase (protein)
Unique Ligands	MG, RP5, SO4, TRS

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1U3E \| pdb_00001u3e	Download File View File

DNA binding and cleavage by the HNH homing endonuclease I-HmuI

Shen, B.W., Landthaler, M., Shub, D.A., Stoddard, B.L.

(2004) J Mol Biology 342: 43-56

Released	2004-08-31
Method	X-RAY DIFFRACTION 2.92 Å
Organisms	Okubovirus SPO1
Macromolecule	HNH homing endonuclease (protein) 36-MER (nucleic acid) 5'-D(CPTPTPAPCPGPTPGPGPGPAPAPTPTPGPCPTPGPAPGPC)-3' (nucleic acid) 5'-D(PGPTPTPAPGPGPCPTPCPAPTPTPAPCPT)-3' (nucleic acid)
Unique Ligands	EDO, MN, SR, TRS

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2CAN \| pdb_00002can	Download File View File

HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH L-CANALINE

Shah, S.A., Shen, B.W., Brunger, A.T.

(1997) Structure 5: 1067-1075

Released	1998-06-03
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	ORNITHINE AMINOTRANSFERASE (protein)
Unique Ligands	CAN, PLP

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2R7E \| pdb_00002r7e	Download File View File

Crystal Structure Analysis of Coagulation Factor VIII

Stoddard, B.L., Shen, B.W.

(2008) Blood 111: 1240-1247

Released	2008-04-15
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor VIII (protein)
Unique Ligands	CA, CU
Unique branched monosaccharides	BMA, MAN, NAG

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3HYI \| pdb_00003hyi	Download File View File

Crystal structure of full-length DUF199/WhiA from Thermatoga maritima

Kaiser, B.K., Clifton, M.C., Shen, B.W., Stoddard, B.L.

(2009) Structure 17: 1368-1376

Released	2009-09-01
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Thermotoga maritima
Macromolecule	Protein DUF199/WhiA (protein)
Unique Ligands	GOL, NA

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3HYJ \| pdb_00003hyj	Download File View File

Crystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA

Kaiser, B.K., Clifton, M.C., Shen, B.W., Stoddard, B.L.

(2009) Structure 17: 1368-1376

Released	2009-09-01
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermotoga maritima
Macromolecule	Protein DUF199/WhiA (protein)
Unique Ligands	CL, GOL, NA

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3LDY \| pdb_00003ldy	Download File View File

An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI

Shen, B.W., Heiter, D., Chan, S.-H., Xu, S.-Y., Wilson, G., Stoddard, B.L.

(2010) Structure 18: 734-743

Released	2010-04-21
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Aquipseudomonas alcaligenes
Macromolecule	restriction endonuclease PacI (protein) DNA (5'-D(GPAPGPGPCPTPTPA)-3') (nucleic acid) DNA (5'-D(PAPTPTPAPAPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	CA, ZN

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3M7K \| pdb_00003m7k	Download File View File

Crystal structure of PacI-DNA Enzyme product complex

Shen, B.W., Stoddard, B.L.

(2010) Structure 18: 734-743

Released	2010-04-21
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Aquipseudomonas alcaligenes
Macromolecule	restriction endonuclease PacI (protein) DNA (5'-D(GPAPGPGPCPTPTPAPAPT)-3') (nucleic acid) DNA (5'-D(PTPAPAPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, MG, NA, PT, SO4, ZN

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3S1S \| pdb_00003s1s	Download File View File

Characterization and crystal structure of the type IIG restriction endonuclease BpuSI

Shen, B.W., Xu, D., Chan, S.-H., Zheng, Y., Zhu, Y., Xu, S.-Y., Stoddard, B.L.

(2011) Nucleic Acids Res 39: 8223-8236

Released	2011-07-13
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Bacillus pumilus
Macromolecule	restriction endonuclease BpuSI (protein)
Unique Ligands	EDO, IOD, MN, SAH

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3U0S \| pdb_00003u0s	Download File View File

Crystal Structure of an Enzyme Redesigned Through Multiplayer Online Gaming: CE6

Bale, J.B., Shen, B.W., Stoddard, B.L.

(2012) Nat Biotechnol 30: 190-192

Released	2012-02-01
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Loligo vulgaris
Macromolecule	Diisopropyl-fluorophosphatase (protein)
Unique Ligands	EPE, GOL, NA, SO4

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4QPZ \| pdb_00004qpz	Download File View File

Crystal structure of the formolase FLS_v2 in space group P 21

Shen, B.W., Siegel, J.B., Stoddard, B.L., Baker, D.

(2015) Proc Natl Acad Sci U S A 112: 3704-3709

Released	2015-03-11
Method	X-RAY DIFFRACTION 3 Å
Organisms	Pseudomonas fluorescens
Macromolecule	Formolase (protein)
Unique Ligands	MG, TPP

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4QQ8 \| pdb_00004qq8	Download File View File

Crystal structure of the formolase FLS in space group P 43 21 2

Shen, B.W., Siegel, J.B., Stoddard, B.L.

(2015) Proc Natl Acad Sci U S A 112: 3704-3709

Released	2015-03-11
Method	X-RAY DIFFRACTION 2.88 Å
Organisms	Pseudomonas fluorescens
Macromolecule	Formolase (protein)
Unique Ligands	EDO, MG, TPP

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4R58 \| pdb_00004r58	Download File View File

Crystal structure of computational designed leucine rich repeats DLRR_A in space group P21

Shen, B.W., Stoddard, B.L.

(2015) Nat Struct Mol Biol 22: 167-174

Released	2015-01-14
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	synthetic construct
Macromolecule	Leucine Rich Repeat protein (protein)

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4R5C \| pdb_00004r5c	Download File View File

Crystal structure of computational designed leucine rich repeats DLRR_E in space group of P212121

Shen, B.W., Stoddard, B.L.

(2015) Nat Struct Mol Biol 22: 167-174

Released	2015-01-07
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	synthetic construct
Macromolecule	Leucine rich repeat protein (protein)
Unique Ligands	EDO

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4R5D \| pdb_00004r5d	Download File View File

Crystal structure of computational designed leucine rich repeats DLRR_G3 in space group F222

Shen, B.W., Stoddard, B.L.

(2015) Nat Struct Mol Biol 22: 167-174

Released	2015-01-07
Method	X-RAY DIFFRACTION 2.53 Å
Organisms	synthetic construct
Macromolecule	Leucine rich repeat protein (protein)
Unique Ligands	EDO, SO4

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4R6F \| pdb_00004r6f	Download File View File

Crystal structure of computational designed protein DLRR_I

Shen, B.W., Stoddard, B.L.

(2015) Nat Struct Mol Biol 22: 167-174

Released	2015-01-07
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	synthetic construct
Macromolecule	Leucine rich repeat DLRR_I (protein)

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4R6G \| pdb_00004r6g	Download File View File

Crystal structure of computational designed leucine rich repeats DLRR_K in space group P22121

Shen, B.W., Stoddard, B.L.

(2015) Nat Struct Mol Biol 22: 167-174

Released	2015-01-07
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	synthetic construct
Macromolecule	leucine rich repeats DLRR_K (protein)
Unique Ligands	CA

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4R6J \| pdb_00004r6j	Download File View File

Crystal structure of computaional designed Lucine rich repeats DLRR_H in space group P212121

Shen, B.W., Stoddard, B.L.

(2015) Nat Struct Mol Biol 22: 167-174

Released	2015-01-07
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	synthetic construct
Macromolecule	Lucine rich repeats DLRR_H (protein)
Unique Ligands	SO4

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5E5O \| pdb_00005e5o	Download File View File

I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions

Shen, B.W.

(2016) J Mol Biology 428: 206-220

Released	2016-01-13
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Sordaria macrospora k-hell synthetic construct
Macromolecule	I-SmaMI LAGLIDADG endonuclease (protein) DNA (25-MER) (nucleic acid) Top strand DNA (25-MER) (nucleic acid)
Unique Ligands	CA, EDO

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5E5P \| pdb_00005e5p	Download File View File

Wild type I-SmaMI in the space group of C121

Shen, B.W.

(2016) J Mol Biology 428: 206-220

Released	2016-01-13
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Sordaria macrospora k-hell
Macromolecule	I-SmaMI LAGLIDADG meganuclease (protein)
Unique Ligands	EDO, PG0

1 to 25 of 44 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

1B0A | pdb_00001b0a

1D7P | pdb_00001d7p

1GBN | pdb_00001gbn

1OAT | pdb_00001oat

1Q33 | pdb_00001q33

1QVJ | pdb_00001qvj

1U3E | pdb_00001u3e

2CAN | pdb_00002can

2R7E | pdb_00002r7e

3HYI | pdb_00003hyi

3HYJ | pdb_00003hyj

3LDY | pdb_00003ldy

3M7K | pdb_00003m7k

3S1S | pdb_00003s1s

3U0S | pdb_00003u0s

4QPZ | pdb_00004qpz

4QQ8 | pdb_00004qq8

4R58 | pdb_00004r58

4R5C | pdb_00004r5c

4R5D | pdb_00004r5d

4R6F | pdb_00004r6f

4R6G | pdb_00004r6g

4R6J | pdb_00004r6j

5E5O | pdb_00005e5o

5E5P | pdb_00005e5p