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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = PO4

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Search Summary

This query matches 58 Structures.

Refinements

Structure Determination Methodology

experimental (58)

Scientific Name of Source Organism

	Streptomyces rubiginosus (22)
	Mus musculus (13)
	Trichoderma reesei (13)
	Oryctolagus cuniculus (3)
	synthetic construct (3)
	Homo sapiens (2)
	Loligo vulgaris (2)
	Xanthobacter autotrophicus (2)
	Equus caballus (1)
	Escherichia coli K-12 (1)

More...

Taxonomy

	Eukaryota (29)
	Bacteria (27)
	other sequences (3)
	Riboviria (1)

Experimental Method

	X-RAY DIFFRACTION (56)
	NEUTRON DIFFRACTION (20)

Polymer Entity Type

	Protein (57)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (38)
	2.0 - 2.5 (23)
	2.5 - 3.0 (1)

Release Date

	2005 - 2009 (6)
	2010 - 2014 (36)
	2015 - 2019 (16)

Enzyme Classification Name

	Isomerases (22)
	Hydrolases (18)
	Transferases (13)
	Oxidoreductases (1)

Symmetry Type

	Asymmetric (31)
	Dihedral (22)
	Cyclic (4)

SCOP Classification

	Alpha and beta proteins (a/b) (25)
	All beta proteins (17)
	Alpha and beta proteins (a+b) (3)
	All alpha proteins (1)
	Artifacts (2)

AllSelected

1 to 25 of 58 Structures

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2GVE \| pdb_00002gve	Download File View File

Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase

Katz, A.K., Li, X., Carrell, H.L., Hanson, B.L., Langan, P., Coates, L., Schoenborn, B.P., Glusker, J.P., Bunick, G.J.

(2006) Proc Natl Acad Sci U S A 103: 8342-8347

Released	2006-05-16
Method	NEUTRON DIFFRACTION 2.2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CO

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2PKY \| pdb_00002pky	Download File View File

The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase

Liu, X., Hanson, L., Langan, P., Viola, R.E.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1000-1008

Released	2007-09-04
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Xanthobacter autotrophicus
Macromolecule	Haloalkane dehalogenase (protein)

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2QWS \| pdb_00002qws	Download File View File

Neutron and X-ray structural studies of short hydrogen bonds in Photoactive Yellow Protein (PYP)

Fisher, S.Z., Langan, P.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1178-1184

Released	2008-03-18
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Halorhodospira halophila
Macromolecule	Photoactive yellow protein (protein)
Unique Ligands	HC4

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2YXP \| pdb_00002yxp	Download File View File

The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase

Liu, X., Hanson, L., Langan, P., Viola, R.E.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1000-1008

Released	2007-09-04
Method	X-RAY DIFFRACTION 1.53 Å
Organisms	Xanthobacter autotrophicus
Macromolecule	Haloalkane dehalogenase (protein)

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3BYC \| pdb_00003byc	Download File View File

Joint neutron and X-ray structure of diisopropyl fluorophosphatase. Deuterium occupancies are 1-Q, where Q is occupancy of H

Blum, M.-M., Mustyakimov, M., Ruterjans, H., Schoenborn, B.P., Langan, P., Chen, J.C.-H.

(2009) Proc Natl Acad Sci U S A 106: 713-718

Released	2009-01-27
Method	X-RAY DIFFRACTION 2.2 Å NEUTRON DIFFRACTION 2.2 Å
Organisms	Loligo vulgaris
Macromolecule	Diisopropyl-fluorophosphatase (protein)
Unique Ligands	CA

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3CWH \| pdb_00003cwh	Download File View File

D-xylose Isomerase in complex with linear product, per-deuterated xylulose

Kovalevsky, A.Y., Langan, P., Glusker, J.P.

(2008) Biochemistry 47: 7595-7597

Released	2008-08-05
Method	NEUTRON DIFFRACTION 2.2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	MG, OH, XUL

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3KBJ \| pdb_00003kbj	Download File View File

Room temperature X-ray structure of apo-D-Xylose Isomerase

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2011) Angew Chem Int Ed Engl 50: 7520-7523

Released	2010-09-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)

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3KBM \| pdb_00003kbm	Download File View File

Room Temperature X-ray structure of D-Xylose Isomerase complexed with 2Cd(2+) co-factors and d12-D-alpha-glucose in the cyclic form

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CD, GLC

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3KBN \| pdb_00003kbn	Download File View File

Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors and d12-D-glucose in the linear form

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 1.53 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	GLO, NI

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3KBS \| pdb_00003kbs	Download File View File

Room Temperature X-ray structure of D-Xylose Isomerase in complex with 2Cd(2+) co-factors

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CD

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3KBV \| pdb_00003kbv	Download File View File

Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	NI

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3KBW \| pdb_00003kbw	Download File View File

Room temperature X-ray mixed-metal structure of D-Xylose Isomerase in complex with Ni(2+) and Mg(2+) co-factors

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	MG, NI

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3KCJ \| pdb_00003kcj	Download File View File

Room temperature neutron structure of apo-D-Xylose Isomerase (refined jointly with X-ray structure 3KBJ)

Kovalevsky, A.Y., Langan, P.

(2011) Angew Chem Int Ed Engl 50: 7520-7523

Released	2010-09-29
Method	NEUTRON DIFFRACTION 1.8 Å X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)

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3KCL \| pdb_00003kcl	Download File View File

Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)

Kovalevsky, A.Y., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	NEUTRON DIFFRACTION 2 Å X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CD, GLC

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3KCO \| pdb_00003kco	Download File View File

Room temperature neutron structure of D-Xylose Isomerase in complex with two Ni2+ cations and d12-D-glucose in the linear form (refined jointly with X-ray structure 3KBN)

Kovalevsky, A.Y., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	NEUTRON DIFFRACTION 1.8 Å X-RAY DIFFRACTION 1.53 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	GLO, NI

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3KGG \| pdb_00003kgg	Download File View File

X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): Perdeuteration of proteins for neutron diffraction

Blum, M.-M., Tomanicek, S.J., John, H., Hanson, B.L., terjans, H.R., Schoenborn, B.P., Langan, P., Chen, J.C.-H.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 379-385

Released	2010-04-07
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Loligo vulgaris
Macromolecule	Diisopropyl-fluorophosphatase (protein)
Unique Ligands	CA

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3L45 \| pdb_00003l45	Download File View File

A Joint Neutron and X-ray structure of Oxidized Amicyanin

Sukumar, N., Mathews, F.S., Langan, P., Davidson, V.L.

(2010) Proc Natl Acad Sci U S A 107: 6817-6822

Released	2010-04-28
Method	NEUTRON DIFFRACTION 1.8 Å X-RAY DIFFRACTION 1.5 Å
Organisms	Paracoccus denitrificans
Macromolecule	Amicyanin (protein)
Unique Ligands	CU

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3QBA \| pdb_00003qba	Download File View File

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Z-DNA (X-ray)

Fenn, T.D., Schnieders, M.J., Mustyakimov, M., Wu, C., Langan, P., Pande, V.S., Brunger, A.T.

(2011) Structure 19: 523-533

Released	2011-03-02
Method	X-RAY DIFFRACTION 1.53 Å NEUTRON DIFFRACTION 1.4 Å
Macromolecule	Z-DNA (nucleic acid)

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3QYS \| pdb_00003qys	Download File View File

Room Temperature X-ray Structure of D-Xylose Isomerase in complex with 0.6Ni2+ cation bound in M2 metal binding site at pH=5.8

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2011) Angew Chem Int Ed Engl 50: 7520-7523

Released	2011-08-17
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	NI

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3QZA \| pdb_00003qza	Download File View File

Joint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2011) Angew Chem Int Ed Engl 50: 7520-7523

Released	2011-08-17
Method	NEUTRON DIFFRACTION 2 Å X-RAY DIFFRACTION 1.7 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	D8U

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3X2U \| pdb_00003x2u	Download File View File

Michaelis-like initial complex of cAMP-dependent Protein Kinase Catalytic Subunit.

Das, A., Langan, P., Gerlits, O., Kovalevsky, A.Y., Heller, W.T.

(2015) Structure 23: 2331-2340

Released	2015-12-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus synthetic construct
Macromolecule	Substrate Peptide (protein) cAMP-dependent protein kinase catalytic subunit alpha (protein)
Unique Ligands	ATP, MG

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3X2V \| pdb_00003x2v	Download File View File

Michaelis-like complex of cAMP-dependent Protein Kinase Catalytic Subunit

Das, A., Langan, P., Gerlits, O., Kovalevsky, A.Y., Heller, W.T.

(2015) Structure 23: 2331-2340

Released	2015-12-16
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Mus musculus synthetic construct
Macromolecule	Substrate Peptide (protein) cAMP-dependent protein kinase catalytic subunit alpha (protein)
Unique Ligands	ATP, CO3, MG

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3X2W \| pdb_00003x2w	Download File View File

Michaelis complex of cAMP-dependent Protein Kinase Catalytic Subunit

Das, A., Langan, P., Gerlits, O., Kovalevsky, A.Y., Heller, W.T.

(2015) Structure 23: 2331-2340

Released	2015-12-16
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mus musculus synthetic construct
Macromolecule	Substrate Peptide (protein) cAMP-dependent protein kinase catalytic subunit alpha (protein)
Unique Ligands	ATP, CO3, MG

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4DH1 \| pdb_00004dh1	Download File View File

Low temperature X-ray structure of cAMP dependent Protein Kinase A catalytic subunit with low Mg2+, ATP and IP20

Kovalevsky, A.Y., Langan, P.

(2012) Acta Crystallogr D Biol Crystallogr 68: 854-860

Released	2012-06-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	cAMP-dependent protein kinase catalytic subunit alpha (protein) cAMP-dependent protein kinase inhibitor alpha (protein)
Unique Ligands	ATP, MG

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4DH3 \| pdb_00004dh3	Download File View File

Low temperature X-ray structure of cAMP dependent Protein Kinase A catalytic subunit with high Mg2+, ATP and IP20

Kovalevsky, A.Y., Langan, P.

(2012) Acta Crystallogr D Biol Crystallogr 68: 854-860

Released	2012-06-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Mus musculus
Macromolecule	cAMP-dependent protein kinase catalytic subunit alpha (protein) cAMP-dependent protein kinase inhibitor alpha (protein)
Unique Ligands	ATP, MG

1 to 25 of 58 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

2GVE | pdb_00002gve

2PKY | pdb_00002pky

2QWS | pdb_00002qws

2YXP | pdb_00002yxp

3BYC | pdb_00003byc

3CWH | pdb_00003cwh

3KBJ | pdb_00003kbj

3KBM | pdb_00003kbm

3KBN | pdb_00003kbn

3KBS | pdb_00003kbs

3KBV | pdb_00003kbv

3KBW | pdb_00003kbw

3KCJ | pdb_00003kcj

3KCL | pdb_00003kcl

3KCO | pdb_00003kco

3KGG | pdb_00003kgg

3L45 | pdb_00003l45

3QBA | pdb_00003qba

3QYS | pdb_00003qys

3QZA | pdb_00003qza

3X2U | pdb_00003x2u

3X2V | pdb_00003x2v

3X2W | pdb_00003x2w

4DH1 | pdb_00004dh1

4DH3 | pdb_00004dh3