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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "PROTEIN BINDING"

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Search Summary

This query matches 38 Structures.

Refinements

Structure Determination Methodology

experimental (38)

Scientific Name of Source Organism

	Arabidopsis thaliana (13)
	Mycobacterium tuberculosis (6)
	Xenopus laevis (6)
	Aquarana catesbeiana (4)
	Streptomyces sp. (3)
	Leishmania donovani BPK282A1 (2)
	Lentzea kentuckyensis (2)
	Shrimp white spot syndrome virus (isolate Tongan) (2)
	Caenorhabditis elegans (1)
	Candida albicans SC5314 (1)

More...

Taxonomy

	Eukaryota (30)
	Bacteria (6)
	Viruses incertae sedis (2)

Experimental Method

X-RAY DIFFRACTION (38)

Polymer Entity Type

	Protein (38)
	DNA (6)

Refinement Resolution (Å)

	1.0 - 1.5 (9)
	1.5 - 2.0 (14)
	2.0 - 2.5 (7)
	2.5 - 3.0 (6)
	3.0 - 3.5 (2)

Release Date

	2010 - 2014 (11)
	2015 - 2019 (13)
	2020 - 2024 (13)
	2025 - 2029 (1)

Enzyme Classification Name

	Isomerases (6)
	Transferases (5)
	Oxidoreductases (4)
	Hydrolases (1)

Symmetry Type

	Cyclic (23)
	Asymmetric (12)
	Octahedral (4)

SCOP Classification

	All alpha proteins (7)
	Alpha and beta proteins (a+b) (6)
	Alpha and beta proteins (a/b) (2)
	Artifacts (2)

AllSelected

1 to 25 of 38 Structures

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3LEL \| pdb_00003lel	Download File View File

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

Wu, B., Vasudevan, D., Davey, C.A.

(2010) Structure 18: 528-536

Released	2010-05-19
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Xenopus laevis
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MN

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3LZ0 \| pdb_00003lz0	Download File View File

Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1)

Vasudevan, D., Chua, E.Y.D., Davey, C.A.

(2010) J Mol Biology 403: 1-10

Released	2010-09-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Xenopus laevis
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	CL, MN

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3LZ1 \| pdb_00003lz1	Download File View File

Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2)

Vasudevan, D., Chua, E.Y.D., Davey, C.A.

(2010) J Mol Biology 403: 1-10

Released	2010-09-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Xenopus laevis
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	CL, MN

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3RFY \| pdb_00003rfy	Download File View File

Crystal structure of arabidopsis thaliana cyclophilin 38 (ATCYP38)

Vasudevan, D., Swaminathan, K.

(2012) Plant Cell 24: 2666-2674

Released	2012-06-13
Method	X-RAY DIFFRACTION 2.39 Å
Organisms	Arabidopsis thaliana
Macromolecule	Peptidyl-prolyl cis-trans isomerase CYP38, chloroplastic (protein)

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3UT9 \| pdb_00003ut9	Download File View File

Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L)

Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A.

(2012) Nucleic Acids Res 40: 6338-6352

Released	2012-04-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Xenopus laevis
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	CL, K, MN

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3UTA \| pdb_00003uta	Download File View File

Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2)

Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A.

(2012) Nucleic Acids Res 40: 6338-6352

Released	2012-04-11
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Xenopus laevis
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	CL, MN

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3UTB \| pdb_00003utb	Download File View File

Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b)

Chua, E.Y.D., Vasudevan, D., Davey, G.E., Wu, B., Davey, C.A.

(2012) Nucleic Acids Res 40: 6338-6352

Released	2012-04-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Xenopus laevis
Macromolecule	Histone H2A (protein) Histone H2B 1.1 (protein) Histone H3.2 (protein) Histone H4 (protein) 146-mer DNA (nucleic acid)
Unique Ligands	MN, SO4

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3WDB \| pdb_00003wdb	Download File View File

N-terminal domain of Mycobacterium tuberculosis ClpC1

Vasudevan, D., Noble, C.G.

(2013) J Biological Chem 288: 30883-30891

Released	2013-09-18
Method	X-RAY DIFFRACTION 1.37 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Probable ATP-dependent Clp protease ATP-binding subunit (protein)
Unique Ligands	FMT

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3WDC \| pdb_00003wdc	Download File View File

N-terminal domain of Mycobacterium tuberculosis ClpC1 bound to Cyclomarin A

Vasudevan, D., Noble, C.G.

(2013) J Biological Chem 288: 30883-30891

Released	2013-09-18
Method	X-RAY DIFFRACTION 1.18 Å
Organisms	Mycobacterium tuberculosis Streptomyces sp.
Macromolecule	Cyclomarin A (protein) Probable ATP-dependent Clp protease ATP-binding subunit (protein)
Unique Ligands	ACT

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3WDD \| pdb_00003wdd	Download File View File

Mutant N-terminal domain of Mycobacterium tuberculosis ClpC1, F2Y, bound to Cyclomarin A

Vasudevan, D., Noble, C.G.

(2013) J Biological Chem 288: 30883-30891

Released	2013-09-18
Method	X-RAY DIFFRACTION 1.18 Å
Organisms	Mycobacterium tuberculosis Streptomyces sp.
Macromolecule	Cyclomarin A (protein) Probable ATP-dependent Clp protease ATP-binding subunit (protein)
Unique Ligands	ACT

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3WDE \| pdb_00003wde	Download File View File

Mutant N-terminal domain of Mycobacterium tuberculosis ClpC1, F80Y, bound to Cyclomarin A

Vasudevan, D., Noble, C.G.

(2013) J Biological Chem 288: 30883-30891

Released	2013-09-18
Method	X-RAY DIFFRACTION 1.44 Å
Organisms	Mycobacterium tuberculosis Streptomyces sp.
Macromolecule	Cyclomarin A (protein) Probable ATP-dependent Clp protease ATP-binding subunit (protein)
Unique Ligands	ACT

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5FOE \| pdb_00005foe	Download File View File

Crystal structure of the C. elegans Protein O-fucosyltransferase 2 (CePOFUT2) double mutant (R298K-R299K) in complex with GDP and the human TSR1 from thrombospondin 1

Valero-Gonzalez, J., Leonhard-Melief, C., Lira-Navarrete, E., Jimenez-Oses, G., Hernandez-Ruiz, C., Pallares, M.C., Yruela, I., Vasudevan, D., Lostao, A., Corzana, F., Takeuchi, H., Haltiwanger, R.S., Hurtado-Guerrero, R.

(2016) Nat Chem Biol 12: 240

Released	2016-01-27
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Caenorhabditis elegans Homo sapiens
Macromolecule	GDP-fucose protein O-fucosyltransferase 2,Thrombospondin-1 (protein)
Unique Ligands	EDO, GDP, NAG

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5GKM \| pdb_00005gkm	Download File View File

Crystal structure of the N-terminal Domain of Caseinolytic protease associated chaperone ClpD from Arabidopsis thaliana

Mohapatra, C., Vasudevan, D.

(2017) Sci Rep 7: 44366-44366

Released	2017-03-22
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Arabidopsis thaliana
Macromolecule	AT5g51070/K3K7_27 (protein)

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5GUI \| pdb_00005gui	Download File View File

Crystal structure of the N-terminal Domain of Caseinolytic protease associated chaperone ClpC1 from Arabidopsis thaliana

Jagdev, M.K., Vasudevan, D.

(2017) Sci Rep 7: 44366-44366

Released	2017-03-22
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Arabidopsis thaliana
Macromolecule	Chaperone protein ClpC1, chloroplastic (protein)
Unique Ligands	PO4

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5XHI \| pdb_00005xhi	Download File View File

Crystal structure of Frog M-ferritin D38A mutant

Jagdev, M.K., Vasudevan, D.

(2017) Biochim Biophys Acta 1865: 1267-1273

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.26 Å
Organisms	Aquarana catesbeiana
Macromolecule	Ferritin, middle subunit (protein)
Unique Ligands	CL, MG

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5XHM \| pdb_00005xhm	Download File View File

Crystal structure of Frog M-ferritin D40A mutant

Jagdev, M.K., Vasudevan, D.

(2017) Biochim Biophys Acta 1865: 1267-1273

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Aquarana catesbeiana
Macromolecule	Ferritin, middle subunit (protein)
Unique Ligands	CL, MG

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5XHN \| pdb_00005xhn	Download File View File

Crystal structure of Frog M-ferritin K104E mutant

Jagdev, M.K., Vasudevan, D.

(2017) Biochim Biophys Acta 1865: 1267-1273

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Aquarana catesbeiana
Macromolecule	Ferritin, middle subunit (protein)
Unique Ligands	CL, MG

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5XHO \| pdb_00005xho	Download File View File

Crystal structure of Frog M-ferritin E135K mutant

Jagdev, M.K., Vasudevan, D.

(2017) Biochim Biophys Acta 1865: 1267-1273

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Aquarana catesbeiana
Macromolecule	Ferritin, middle subunit (protein)
Unique Ligands	CL, MG

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5ZWY \| pdb_00005zwy	Download File View File

Ribokinase from Leishmania donovani

Gatreddi, S., Vasudevan, D., Qureshi, I.A.

(2019) Int J Biol Macromol 136: 253-265

Released	2019-05-22
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Leishmania donovani BPK282A1
Macromolecule	Ribokinase (protein)
Unique Ligands	CL, GOL, NA

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6A8C \| pdb_00006a8c	Download File View File

Ribokinase from Leishmania donovani with ADP

Gatreddi, S., Vasudevan, D., Qureshi, I.A.

(2019) Int J Biol Macromol 136: 253-265

Released	2019-07-10
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Leishmania donovani BPK282A1
Macromolecule	Ribokinase (protein)
Unique Ligands	ADP, CL, GOL, NA

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6ICE \| pdb_00006ice	Download File View File

Crystal structure of Hamster MIF

Sundaram, R., Vasudevan, D.

(2019) Sci Rep 9: 15507-15507

Released	2019-09-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mesocricetus auratus
Macromolecule	Macrophage migration inhibitory factor (protein)

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6J2M \| pdb_00006j2m	Download File View File

Crystal structure of AtFKBP53 C-terminal domain

Singh, A.K., Vasudevan, D.

(2020) Nucleic Acids Res 48: 1531-1550

Released	2019-12-04
Method	X-RAY DIFFRACTION 1.13 Å
Organisms	Arabidopsis thaliana
Macromolecule	Peptidyl-prolyl cis-trans isomerase FKBP53 (protein)
Unique Ligands	CL, FK5