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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Makde, R.D."

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Search Summary

This query matches 69 Structures.

Refinements

Structure Determination Methodology

experimental (69)

Scientific Name of Source Organism

	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (24)
	Salmonella enterica subsp. enterica serovar Typhimurium (7)
	Sphingobium sp. 20006FA (5)
	Leishmania major (4)
	Xanthomonas campestris pv. campestris str. ATCC 33913 (4)
	Drosophila melanogaster (3)
	Homo sapiens (3)
	Saccharomyces cerevisiae S288C (3)
	Xenopus laevis (3)
	Calotropis gigantea (2)

More...

Taxonomy

	Bacteria (50)
	Eukaryota (19)

Experimental Method

X-RAY DIFFRACTION (69)

Polymer Entity Type

	Protein (69)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (18)
	2.0 - 2.5 (34)
	2.5 - 3.0 (8)
	3.0 - 3.5 (1)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (9)
	2010 - 2014 (2)
	2015 - 2019 (32)
	2020 - 2024 (25)
	2025 - 2029 (1)

Enzyme Classification Name

Hydrolases (37)

Symmetry Type

	Asymmetric (23)
	Cyclic (26)
	Dihedral (20)

SCOP Classification

	Alpha and beta proteins (a/b) (10)
	All alpha proteins (3)
	Artifacts (6)
	Alpha and beta proteins (a+b) (1)

AllSelected

1 to 25 of 69 Structures

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1Z5G \| pdb_00001z5g	Download File View File

Crystal structure of Salmonella typhimurium AphA protein

Makde, R.D., Kumar, V.

(2007) Arch Biochem Biophys 464: 70-79

Released	2006-03-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	AphA protein (protein)
Unique Ligands	MG, PO4

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1Z5U \| pdb_00001z5u	Download File View File

Crystal structure of S. typhimurium AphA complexed with cyclic-AMP

Makde, R.D., Kumar, V.

To be published

Released	2006-03-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	AphA protein (protein)
Unique Ligands	CMP, MG

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1Z88 \| pdb_00001z88	Download File View File

Crystal structure of Lys154Arg mutant of mature AphA of S. typhimurium

Makde, R.D., Gupta, G.D., Kumar, V.

(2007) Arch Biochem Biophys 464: 70-79

Released	2006-04-04
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	AphA protein (protein)
Unique Ligands	MG

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2A96 \| pdb_00002a96	Download File View File

Crystal structure of phosphate tethered PhoN of S. typhimurium

Makde, R.D., Mahajan, S.K., Kumar, V.

(2007) Biochemistry 46: 2079-2090

Released	2006-05-23
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	class A nonspecific acid phosphatase PhoN (protein)
Unique Ligands	PO4

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2AKC \| pdb_00002akc	Download File View File

Crystal structure of tungstate complex of the PhoN protein from S. typhimurium

Makde, R.D., Kumar, V.

(2007) Biochemistry 46: 2079-2090

Released	2006-05-23
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	class A nonspecific acid phosphatase PhoN (protein)
Unique Ligands	WO4

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2AUT \| pdb_00002aut	Download File View File

Crystal structure of Lys154Asn mutant of mature AphA of S. typhimurium

Makde, R.D., Gupta, G.D., Kumar, V.

(2007) Arch Biochem Biophys 464: 70-79

Released	2006-09-05
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	AphA (protein)
Unique Ligands	MG, NA, PO4

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2IPB \| pdb_00002ipb	Download File View File

Crystal structure of T159D mutant of S. Typhimurium PhoN protein

Makde, R.D., Kumar, V.

(2007) Biochemistry 46: 2079-2090

Released	2007-03-06
Method	X-RAY DIFFRACTION 2.23 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	Class A nonspecific acid phosphatase PhoN (protein)

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2QRX \| pdb_00002qrx	Download File View File

Crystal structure of Drosophila melanogaster Translin protein

Gupta, G.D., Makde, R.D., Kumar, V.

(2008) FEBS J 275: 4235-4249

Released	2008-08-05
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Drosophila melanogaster
Macromolecule	GM27569p (protein)

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2QVA \| pdb_00002qva	Download File View File

Crystal structure of Drosophila melanogaster Translin protein

Gupta, G.D., Makde, R.D., Kumar, V.

(2008) FEBS J 275: 4235-4249

Released	2008-08-05
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Drosophila melanogaster
Macromolecule	GM27569p (protein)

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3MVD \| pdb_00003mvd	Download File View File

Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle

Makde, R.D., England, J.R., Yennawar, H.P., Tan, S.

(2010) Nature 467: 562-566

Released	2010-08-25
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Drosophila melanogaster Xenopus laevis
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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4R60 \| pdb_00004r60	Download File View File

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris

Kumar, A., Ghosh, B., Are, V.N., Jamdar, S.N., Makde, R.D., Sharma, S.M.

To be published

Released	2014-09-17
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Xanthomonas campestris pv. campestris str. ATCC 33913
Macromolecule	Proline dipeptidase (protein)
Unique Ligands	MN, NA, PO4

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5CIK \| pdb_00005cik	Download File View File

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris in citrate condition

Kumar, A., Are, V., Ghosh, B., Agrawal, U., Jamdar, S., Makde, R.D.

To be published

Released	2016-07-20
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Xanthomonas campestris pv. campestris str. ATCC 33913
Macromolecule	Proline dipeptidase (protein)
Unique Ligands	CIT, GOL

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5CNX \| pdb_00005cnx	Download File View File

Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12

Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.D.

(2018) Proteins

Released	2016-07-20
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia coli K-12
Macromolecule	Aminopeptidase YpdF (protein)
Unique Ligands	CAC, GOL, NA, ZN

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5FCF \| pdb_00005fcf	Download File View File

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound

Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.D.

(2017) Biochim Biophys Acta 1865: 153-164

Released	2016-12-07
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Escherichia coli Xanthomonas campestris pv. campestris str. ATCC 33913
Macromolecule	GLY-GLY-GLY (protein) Proline dipeptidase (protein)
Unique Ligands	GOL, MN, PEG, PO4

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5FCH \| pdb_00005fch	Download File View File

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Zn bound

Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.D.

(2017) Biochim Biophys Acta 1865: 153-164

Released	2016-12-07
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Escherichia coli Xanthomonas campestris pv. campestris str. ATCC 33913
Macromolecule	GLY-GLY-GLY (protein) Proline dipeptidase (protein)
Unique Ligands	GOL, PEG, PO4, ZN

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5GIQ \| pdb_00005giq	Download File View File

Xaa-Pro peptidase from Deinococcus radiodurans, Zinc bound

Are, V.N., Singh, R., Kumar, A., Ghosh, B., Jamdar, S.N., Makde, R.D.

(2018) Proteins

Released	2017-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Proline dipeptidase (protein)
Unique Ligands	PO4, ZN

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5GIU \| pdb_00005giu	Download File View File

Crystal structure of Xaa-Pro peptidase from Deinococcus radiodurans, metal-free active site

Are, V.N., Kumar, A., Singh, R., Ghosh, B., Jamdar, S.N., Makde, R.D.

To be published

Released	2017-06-28
Method	X-RAY DIFFRACTION 1.61 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Proline dipeptidase (protein)
Unique Ligands	NA, PO4

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5GIV \| pdb_00005giv	Download File View File

Crystal structure of M32 carboxypeptidase from Deinococcus radiodurans R1

Sharma, B., Singh, R., Yadav, P., Ghosh, B., Kumar, A., Jamdar, S.N., Makde, R.D.

(2017) Biochim Biophys Acta 1865: 1406-1415

Released	2017-07-12
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Carboxypeptidase 1 (protein)
Unique Ligands	ACT, ZN

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5X49 \| pdb_00005x49	Download File View File

Crystal Structure of Human mitochondrial X-prolyl Aminopeptidase (XPNPEP3)

Singh, R., Kumar, A., Ghosh, B., Jamdar, S., Makde, R.D.

(2017) J Biological Chem 292: 10035-10047

Released	2017-05-17
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Probable Xaa-Pro aminopeptidase 3 (protein)
Unique Ligands	01B, 12P, DMS, EDO, MN

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5XEV \| pdb_00005xev	Download File View File

Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus radiodurans

Are, V.N., Kumar, A., Ghosh, B., Makde, R.D.

(2017) Proteins 85: 2239-2251

Released	2017-10-18
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Xaa-Pro dipeptidase,Peptidase-related protein (protein)
Unique Ligands	ACT, CL, EDO, PO4, ZN

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5YZM \| pdb_00005yzm	Download File View File

Crystal structure of S9 peptidase (inactive form) from Deinococcus radiodurans R1

Yadav, P., Jamdar, S.N., Kumar, A., Ghosh, B., Makde, R.D.

(2019) J Biological Chem 294: 89-100

Released	2018-11-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Acyl-peptide hydrolase, putative (protein)
Unique Ligands	ACT

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5YZN \| pdb_00005yzn	Download File View File

Crystal structure of S9 peptidase (active form) from Deinococcus radiodurans R1

Yadav, P., Jamdar, S.N., Kumar, A., Ghosh, B., Makde, R.D.

(2019) J Biological Chem 294: 89-100

Released	2018-11-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Acyl-peptide hydrolase, putative (protein)

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5YZO \| pdb_00005yzo	Download File View File

Crystal structure of S9 peptidase mutant (S514A) from Deinococcus radiodurans R1

Yadav, P., Jamdar, S.N., Kumar, A., Ghosh, B., Makde, R.D.

(2019) J Biological Chem 294: 89-100

Released	2018-11-14
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Acyl-peptide hydrolase, putative (protein)
Unique Ligands	DMS, GOL

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5Z40 \| pdb_00005z40	Download File View File

Crystal structure of pyrrolidone carboxylate peptidase I from Deionococcus radiodurans R1

Agrawal, R., Kumar, A., Makde, R.D.

To be published

Released	2019-01-16
Method	X-RAY DIFFRACTION 1.837 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Pyrrolidone-carboxylate peptidase (protein)

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5Z47 \| pdb_00005z47	Download File View File

Crystal structure of pyrrolidone carboxylate peptidase I with disordered loop A from Deinococcus radiodurans R1

Agrawal, R., Kumar, A., Kumar, A., Makde, R.D.

(2019) Acta Crystallogr D Struct Biol 75: 308-316

Released	2019-01-16
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	Pyrrolidone-carboxylate peptidase (protein)
Unique Ligands	DMS

1 to 25 of 69 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

1Z5G | pdb_00001z5g

1Z5U | pdb_00001z5u

1Z88 | pdb_00001z88

2A96 | pdb_00002a96

2AKC | pdb_00002akc

2AUT | pdb_00002aut

2IPB | pdb_00002ipb

2QRX | pdb_00002qrx

2QVA | pdb_00002qva

3MVD | pdb_00003mvd

4R60 | pdb_00004r60

5CIK | pdb_00005cik

5CNX | pdb_00005cnx

5FCF | pdb_00005fcf

5FCH | pdb_00005fch

5GIQ | pdb_00005giq

5GIU | pdb_00005giu

5GIV | pdb_00005giv

5X49 | pdb_00005x49

5XEV | pdb_00005xev

5YZM | pdb_00005yzm

5YZN | pdb_00005yzn

5YZO | pdb_00005yzo

5Z40 | pdb_00005z40

5Z47 | pdb_00005z47