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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kim, J.K."

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Search Summary

This query matches 83 Structures.

Refinements

Structure Determination Methodology

experimental (83)

Scientific Name of Source Organism

	Homo sapiens (49)
	Xanthomonas oryzae pv. oryzae KACC 10331 (8)
	Pseudomonas sp. GK16 (6)
	Acetivibrio thermocellus ATCC 27405 (3)
	Halalkalibacterium halodurans (3)
	synthetic construct (3)
	Escherichia coli APEC O1 (2)
	Escherichia coli str. 'clone D i14 (2)
	Pseudomonas sp. SY-77-1 (2)
	Xanthomonas oryzae pv. oryzae MAFF 311018 (2)

More...

Taxonomy

	Eukaryota (50)
	Bacteria (30)
	other sequences (3)

Experimental Method

	X-RAY DIFFRACTION (81)
	SOLID-STATE NMR (1)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (83)

Refinement Resolution (Å)

	0.5 - 1.0 (3)
	1.0 - 1.5 (45)
	1.5 - 2.0 (6)
	2.0 - 2.5 (17)
	2.5 - 3.0 (10)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (9)
	2010 - 2014 (21)
	2015 - 2019 (1)
	2020 - 2024 (51)

Enzyme Classification Name

	Lyases (52)
	Hydrolases (11)
	Isomerases (6)
	Ligases (4)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (66)
	Cyclic (14)
	Dihedral (6)

SCOP Classification

	Alpha and beta proteins (a+b) (12)
	Alpha and beta proteins (a/b) (16)
	All beta proteins (24)
	All alpha proteins (1)

AllSelected

1 to 25 of 83 Structures

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1OR0 \| pdb_00001or0	Download File View File

Crystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight into Autoproteolytic Activation

Kim, J.K., Yang, I.S., Rhee, S., Dauter, Z., Lee, Y.S., Park, S.S., Kim, K.H.

(2003) Biochemistry 42: 4084-4093

Released	2004-03-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Pseudomonas sp. SY-77-1
Macromolecule	Glutaryl 7-Aminocephalosporanic Acid Acylase (protein) glutaryl acylase (protein)
Unique Ligands	EDO

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2ADV \| pdb_00002adv	Download File View File

Crystal Structures Of Glutaryl 7-Aminocephalosporanic Acid Acylase: mutational study of activation mechanism

Kim, J.K., Yang, I.S., Shin, H.J., Cho, K.J., Ryu, E.K., Kim, S.H., Park, S.S., Kim, K.H.

(2006) Proc Natl Acad Sci U S A 103: 1732-1737

Released	2006-01-24
Method	X-RAY DIFFRACTION 2.244 Å
Organisms	Pseudomonas sp. GK16
Macromolecule	Glutaryl 7- Aminocephalosporanic Acid Acylase (protein)

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2AE3 \| pdb_00002ae3	Download File View File

Glutaryl 7-Aminocephalosporanic Acid Acylase: mutational study of activation mechanism

Kim, J.K., Yang, I.S., Shin, H.J., Cho, K.J., Ryu, E.K., Kim, S.H., Park, S.S., Kim, K.H.

(2006) Proc Natl Acad Sci U S A 103: 1732-1737

Released	2006-01-24
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Pseudomonas sp. GK16
Macromolecule	Glutaryl 7-Aminocephalosporanic Acid Acylase (protein)
Unique Ligands	GOL

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2AE4 \| pdb_00002ae4	Download File View File

Glutaryl 7-Aminocephalosporanic Acid Acylase: mutational study of activation mechanism

Kim, J.K., Yang, I.S., Shin, H.J., Cho, K.J., Ryu, E.K., Kim, S.H., Park, S.S., Kim, K.H.

(2006) Proc Natl Acad Sci U S A 103: 1732-1737

Released	2006-01-24
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pseudomonas sp. GK16
Macromolecule	Glutaryl 7-Aminocephalosporanic Acid Acylase (protein)
Unique Ligands	GOL, SO4

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2AE5 \| pdb_00002ae5	Download File View File

Glutaryl 7-Aminocephalosporanic Acid Acylase: mutational study of activation mechanism

Kim, J.K., Yang, I.S., Shin, H.J., Cho, K.J., Ryu, E.K., Kim, S.H., Park, S.S., Kim, K.H.

(2006) Proc Natl Acad Sci U S A 103: 1732-1737

Released	2006-01-24
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Pseudomonas sp. GK16
Macromolecule	Glutaryl 7-Aminocephalosporanic Acid Acylase (protein)
Unique Ligands	GOL, SO4

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2LN4 \| pdb_00002ln4	Download File View File

Insight into the antimicrobial activities based on the Structure-activity relationships of coprisin isolated from the Dung Beetle, Copris tripartitus

Kim, Y., Kim, J.K., Lee, E.

(2012) Biochim Biophys Acta

Released	2012-11-28
Method	SOLUTION NMR
Organisms	Copris tripartitus
Macromolecule	Coprisin (protein)

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2N0A \| pdb_00002n0a	Download File View File

Atomic-resolution structure of alpha-synuclein fibrils

Tuttle, M.D., Comellas, G., Nieuwkoop, A.J., Covell, D.J., Berthold, D.A., Kloepper, K.D., Courtney, J.M., Kim, J.K., Schwieters, C.D., Lee, V.M., George, J.M., Rienstra, C.M.

(2016) Nat Struct Mol Biol 23: 409-415

Released	2016-03-23
Method	SOLID-STATE NMR
Organisms	Homo sapiens
Macromolecule	Alpha-synuclein (protein)

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3DKU \| pdb_00003dku	Download File View File

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

Hong, M.K., Kim, J.K., Jung, J.H., Jung, J.W., Choi, J.Y., Kang, L.W.

To be published

Released	2009-06-30
Method	X-RAY DIFFRACTION 2.69 Å
Organisms	Escherichia coli APEC O1
Macromolecule	Putative phosphohydrolase (protein)

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3E5N \| pdb_00003e5n	Download File View File

Crystal structure of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331

Doan, T.N.T., Kim, J.K., Kim, H.S., Ahn, Y.J., Kim, J.G., Lee, B.M., Kang, L.W.

To be published

Released	2009-08-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Xanthomonas oryzae pv. oryzae MAFF 311018
Macromolecule	D-alanine-D-alanine ligase A (protein)

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3E6G \| pdb_00003e6g	Download File View File

Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae

Ngo, H.P.T., Kim, J.K., Kim, H.S., Jung, J.H., Ahn, Y.J., Kim, J.G., Lee, B.M., Kang, H.W., Kang, L.W.

To be published

Released	2009-08-18
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Xanthomonas oryzae pv. oryzae
Macromolecule	Cystathionine gamma-lyase-like protein (protein)

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3HE8 \| pdb_00003he8	Download File View File

Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B

Kang, L.W., Kim, J.K., Jung, J.H., Hong, M.K.

(2011) Appl Microbiol Biotechnol 90: 517-527

Released	2009-11-10
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Acetivibrio thermocellus ATCC 27405
Macromolecule	Ribose-5-phosphate isomerase (protein)
Unique Ligands	GOL

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3HEE \| pdb_00003hee	Download File View File

Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B and ribose-5-phosphate

Kang, L.W., Kim, J.K., Jung, J.H., Hong, M.K.

(2011) Appl Microbiol Biotechnol 90: 517-527

Released	2009-11-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Acetivibrio thermocellus ATCC 27405
Macromolecule	Ribose-5-phosphate isomerase (protein)
Unique Ligands	R5P

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3JTQ \| pdb_00003jtq	Download File View File

Mutations in Cephalosporin Acylase Affecting Stability and Autoproteolysis

Cho, K.J., Kim, J.K., Lee, J.H., Shin, H.J., Park, S.S., Kim, K.H.

(2009) Biochem Biophys Res Commun 390: 342-348

Released	2010-01-26
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pseudomonas sp. GK16
Macromolecule	Glutaryl 7-aminocephalosporanic acid acylase (protein)
Unique Ligands	GOL

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3JTR \| pdb_00003jtr	Download File View File

Mutations in Cephalosporin Acylase Affecting Stability and Autoproteolysis

Cho, K.J., Kim, J.K., Lee, J.H., Shin, H.J., Park, S.S., Kim, K.H.

(2009) Biochem Biophys Res Commun 390: 342-348

Released	2010-01-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pseudomonas sp. GK16
Macromolecule	Glutaryl 7-aminocephalosporanic acid acylase (protein)
Unique Ligands	GOL

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3PH3 \| pdb_00003ph3	Download File View File

Clostridium thermocellum Ribose-5-Phosphate Isomerase B with d-ribose

Jung, J., Kim, J.K., Yeom, S.J., Ahn, Y.J., Oh, D.K., Kang, L.W.

(2011) Appl Microbiol Biotechnol 90: 517-527

Released	2011-06-22
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Acetivibrio thermocellus ATCC 27405
Macromolecule	Ribose-5-phosphate isomerase (protein)
Unique Ligands	RB5

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3R5F \| pdb_00003r5f	Download File View File

Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with ATP

Doan, T.T.N., Kim, J.K., Kang, L.W.

To be published

Released	2011-05-25
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Xanthomonas oryzae pv. oryzae KACC 10331
Macromolecule	D-alanine--D-alanine ligase 1 (protein)
Unique Ligands	ATP, MG

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3RFC \| pdb_00003rfc	Download File View File

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

Doan, T.T.N., Kim, J.K., Ahn, Y.J., Kang, L.W.

To be published

Released	2011-05-04
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Xanthomonas oryzae pv. oryzae MAFF 311018
Macromolecule	D-alanine--D-alanine ligase 1 (protein)
Unique Ligands	ADP, MG

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3S8R \| pdb_00003s8r	Download File View File

Crystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight into Autoproteolytic Activation

Kim, J.K., Yang, I.S., Park, S.S., Kim, K.H.

(2003) Biochemistry 42: 4084-4093

Released	2011-07-06
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pseudomonas sp. SY-77-1
Macromolecule	Glutaryl-7-aminocephalosporanic-acid acylase (protein)
Unique Ligands	GOL

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3SHD \| pdb_00003shd	Download File View File

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

Hong, M.K., Kim, J.K., Kang, L.W.

To be published

Released	2012-06-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli APEC O1
Macromolecule	Phosphatase nudJ (protein)
Unique Ligands	MN, SO4

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3UU0 \| pdb_00003uu0	Download File View File

Crystal structure of L-rhamnose isomerase from Bacillus halodurans in complex with Mn

Doan, T.T.N., Prabhu, P., Kim, J.K., Jeya, M., Kang, L.W., Lee, J.K.

(2014) FEBS J 281: 3446-3459

Released	2012-02-01
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Halalkalibacterium halodurans
Macromolecule	L-rhamnose isomerase (protein)
Unique Ligands	MN

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3UVA \| pdb_00003uva	Download File View File

Crystal structure of L-rhamnose isomerase mutant W38F from Bacillus halodurans in complex with Mn

Doan, T.T.N., Prabhu, P., Jeya, M., Kim, J.K., Kang, L.W., Lee, J.K.

(2014) FEBS J 281: 3446-3459

Released	2012-12-05
Method	X-RAY DIFFRACTION 2.69 Å
Organisms	Halalkalibacterium halodurans
Macromolecule	L-Rhamnose isomerase (protein)
Unique Ligands	MN

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3UXI \| pdb_00003uxi	Download File View File

Crystal structure of L-rhamnose isomerase W38A mutant from Bacillus halodurans

Doan, T.T.N., Prabhu, P., Kim, J.K., Jeya, M., Kang, L.W., Lee, J.K.

(2014) FEBS J 281: 3446-3459

Released	2012-12-26
Method	X-RAY DIFFRACTION 2.73 Å
Organisms	Halalkalibacterium halodurans
Macromolecule	L-Rhamnose isomerase (protein)
Unique Ligands	MN

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4FXB \| pdb_00004fxb	Download File View File

Crystal structure of CYP105N1 from Streptomyces coelicolor: a cytochrome P450 oxidase in the coelibactin siderophore biosynthetic pathway

Hong, M.K., Lim, Y.R., Kim, J.K., Kim, D.H., Kang, L.W.

(2012) Arch Biochem Biophys 528: 111-117

Released	2012-11-14
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Streptomyces coelicolor A3(2)
Macromolecule	Putative cytochrome P450 (protein)
Unique Ligands	HEM

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4IXS \| pdb_00004ixs	Download File View File

Native structure of xometc at ph 5.2

Ngo, H.P.T., Kim, J.K., Kang, L.W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 596-606

Released	2014-01-29
Method	X-RAY DIFFRACTION 2.29 Å
Organisms	Xanthomonas oryzae pv. oryzae KACC 10331
Macromolecule	Cystathionine gamma-lyase-like protein (protein)
Unique Ligands	CO3, GOL

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4IXZ \| pdb_00004ixz	Download File View File

Native structure of cystathionine gamma lyase (XometC) from xanthomonas oryzae pv. oryzae at pH 9.0

Ngo, H.P.T., Kim, J.K., Kang, L.W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 596-606

Released	2014-01-29
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Xanthomonas oryzae pv. oryzae KACC 10331
Macromolecule	Cystathionine gamma-lyase-like protein (protein)
Unique Ligands	BCT, BME, GOL

1 to 25 of 83 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

1OR0 | pdb_00001or0

2ADV | pdb_00002adv

2AE3 | pdb_00002ae3

2AE4 | pdb_00002ae4

2AE5 | pdb_00002ae5

2LN4 | pdb_00002ln4

2N0A | pdb_00002n0a

3DKU | pdb_00003dku

3E5N | pdb_00003e5n

3E6G | pdb_00003e6g

3HE8 | pdb_00003he8

3HEE | pdb_00003hee

3JTQ | pdb_00003jtq

3JTR | pdb_00003jtr

3PH3 | pdb_00003ph3

3R5F | pdb_00003r5f

3RFC | pdb_00003rfc

3S8R | pdb_00003s8r

3SHD | pdb_00003shd

3UU0 | pdb_00003uu0

3UVA | pdb_00003uva

3UXI | pdb_00003uxi

4FXB | pdb_00004fxb

4IXS | pdb_00004ixs

4IXZ | pdb_00004ixz