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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Huynh, K.-H."

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Search Summary

This query matches 49 Structures.

Refinements

Structure Determination Methodology

experimental (49)

Scientific Name of Source Organism

	Homo sapiens (45)
	Tequatrovirus T4 (7)
	Saccharomyces cerevisiae (3)
	Enterobacteria phage RB59 (1)
	Saccharomyces cerevisiae S288C (1)

Taxonomy

	Eukaryota (49)
	Duplodnaviria (8)

Experimental Method

	X-RAY DIFFRACTION (33)
	ELECTRON MICROSCOPY (16)

Polymer Entity Type

Protein (49)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (10)
	2.0 - 2.5 (7)
	2.5 - 3.0 (6)
	3.0 - 3.5 (13)
	3.5 - 4.0 (8)

Release Date

	2005 - 2009 (3)
	2010 - 2014 (12)
	2015 - 2019 (8)
	2020 - 2024 (26)

Enzyme Classification Name

	Transferases (29)
	Ligases (9)
	Hydrolases (8)

Symmetry Type

	Asymmetric (48)
	Cyclic (3)

SCOP Classification

	Alpha and beta proteins (a+b) (4)
	Artifacts (3)
	Small proteins (3)
	All alpha proteins (1)
	Multi-domain proteins (alpha and beta) (1)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 49 Structures

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3DPL \| pdb_00003dpl	Download File View File

Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation.

Duda, D.M., Schulman, B.A.

(2008) Cell 134: 995-1006

Released	2008-09-30
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Cullin-5 (protein) RING-box protein 1 (protein)
Unique Ligands	ZN

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3DQV \| pdb_00003dqv	Download File View File

Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation

Duda, D.M., Borg, L.A., Scott, D.C., Hunt, H.W., Hammel, M., Schulman, B.A.

(2008) Cell 134: 995-1006

Released	2008-09-30
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Cullin-5 (protein) NEDD8 (protein) Rbx1 (protein)
Unique Ligands	ZN

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3FN1 \| pdb_00003fn1	Download File View File

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification.

Huang, D.T., Ayrault, O., Hunt, H.W., Taherbhoy, A.M., Duda, D.M., Scott, D.C., Borg, L.A., Neale, G., Murray, P.J., Roussel, M.F., Schulman, B.A.

(2009) Mol Cell 33: 483-495

Released	2009-03-17
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	NEDD8-activating enzyme E1 catalytic subunit (protein) NEDD8-conjugating enzyme UBE2F (protein)

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3JVZ \| pdb_00003jvz	Download File View File

E2~Ubiquitin-HECT

Souphron, J., Kamadurai, H.B., Schulman, B.A.

(2009) Mol Cell 36: 1095-1102

Released	2010-01-12
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase NEDD4-like (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)

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3JW0 \| pdb_00003jw0	Download File View File

E2~Ubiquitin-HECT

Kamadurai, H.B., Schulman, B.A.

(2009) Mol Cell 36: 1095-1102

Released	2010-01-12
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase NEDD4-like (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)

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3O2P \| pdb_00003o2p	Download File View File

A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB)

Scott, D.C., Monda, J.K., Grace, C.R.R., Duda, D.M., Kriwacki, R.W., Kurz, T., Schulman, B.A.

(2010) Mol Cell 39: 784-796

Released	2010-09-15
Method	X-RAY DIFFRACTION 2.233 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cell division control protein 53 (protein) Defective in cullin neddylation protein 1 (protein)
Unique Ligands	GOL

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3O2U \| pdb_00003o2u	Download File View File

S. cerevisiae Ubc12

Scott, D.C., Monda, J.K., Grace, C.R.R., Duda, D.M., Kriwacki, R.W., Kurz, T., Schulman, B.A.

(2010) Mol Cell 39: 784-796

Released	2010-09-15
Method	X-RAY DIFFRACTION 2.003 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	NEDD8-conjugating enzyme UBC12 (protein)
Unique Ligands	GOL

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3O6B \| pdb_00003o6b	Download File View File

A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) low resolution

Scott, D.C., Monda, J.K., Grace, C.R.R., Duda, D.M., Kriwacki, R.W., Kurz, T., Schulman, B.A.

(2010) Mol Cell 39: 784-796

Released	2010-09-15
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cell division control protein 53 (protein) Defective in cullin neddylation protein 1 (protein)

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3RTR \| pdb_00003rtr	Download File View File

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases

Calabrese, M.F., Scott, D.C., Duda, D.M., Grace, C.R., Kurinov, I., Kriwacki, R.W., Schulman, B.A.

(2011) Nat Struct Mol Biol 18: 947-949

Released	2011-07-20
Method	X-RAY DIFFRACTION 3.21 Å
Organisms	Homo sapiens
Macromolecule	Cullin-1 (protein) E3 ubiquitin-protein ligase RBX1 (protein)
Unique Ligands	ZN

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3TDI \| pdb_00003tdi	Download File View File

yeast Cul1WHB-Dcn1P acetylated Ubc12N complex

Scott, D.C., Monda, J.K., Bennett, E.J., Harper, J.W., Schulman, B.A.

(2011) Science 334: 674-678

Released	2011-10-12
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Defective in cullin neddylation protein 1 (protein) NEDD8-conjugating enzyme UBC12 (protein)

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3TDU \| pdb_00003tdu	Download File View File

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex

Scott, D.C., Monda, J.K., Bennett, E.J., Harper, J.W., Schulman, B.A.

(2011) Science 334: 674-678

Released	2011-10-12
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	Cullin-1 (protein) DCN1-like protein 1 (protein) NEDD8-conjugating enzyme Ubc12 (protein)

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3TDZ \| pdb_00003tdz	Download File View File

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-stapled acetylated Ubc12N complex

Scott, D.C., Monda, J.K., Bennett, E.J., Harper, J.W., Schulman, B.A.

(2011) Science 334: 674-678

Released	2011-10-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Cullin-1 (protein) DCN1-like protein 1 (protein) STAPLED PEPTIDE (protein)

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4GAO \| pdb_00004gao	Download File View File

DCNL complex with N-terminally acetylated NEDD8 E2 peptide

Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A.

(2013) Structure 21: 42-53

Released	2012-11-28
Method	X-RAY DIFFRACTION 3.28 Å
Organisms	Homo sapiens
Macromolecule	DCN1-like protein 2 (protein) NEDD8-conjugating enzyme Ubc12 (protein)
Unique Ligands	BR

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4GBA \| pdb_00004gba	Download File View File

DCNL complex with N-terminally acetylated NEDD8 E2 peptide

Monda, J.K., Scott, D.C., Miller, D.J., Harper, J.W., Bennett, E.J., Schulman, B.A.

(2013) Structure 21: 42-53

Released	2012-11-28
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	DCN1-like protein 3 (protein) NEDD8-conjugating enzyme UBE2F (protein)

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4P5O \| pdb_00004p5o	Download File View File

Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action

Scott, D.C., Schulman, B.A.

(2014) Cell 157: 1671-1684

Released	2014-07-02
Method	X-RAY DIFFRACTION 3.1071 Å
Organisms	Homo sapiens
Macromolecule	Cullin-1 (protein) DCN1-like protein 1 (protein) E3 ubiquitin-protein ligase RBX1 (protein) NEDD8 (protein) NEDD8-conjugating enzyme Ubc12 (protein)
Unique Ligands	ZN

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5V83 \| pdb_00005v83	Download File View File

Structure of DCN1 bound to NAcM-HIT

Guy, R.K., Schulman, B.A., Scott, D.C., Hammill, J.T.

(2017) Nat Chem Biol 13: 850-857

Released	2017-05-24
Method	X-RAY DIFFRACTION 2.002 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Lysozyme,DCN1-like protein 1 chimera (protein)
Unique Ligands	8Z7

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5V86 \| pdb_00005v86	Download File View File

Structure of DCN1 bound to NAcM-OPT

Guy, R.K., Schulman, B.A., Scott, D.C., Hammill, J.T.

(2017) Nat Chem Biol 13: 850-857

Released	2017-05-24
Method	X-RAY DIFFRACTION 1.374 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Lysozyme,DCN1-like protein 1 (protein)
Unique Ligands	8ZA

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5V88 \| pdb_00005v88	Download File View File

Structure of DCN1 bound to NAcM-COV

Guy, R.K., Schulman, B.A., Scott, D.C., Hammill, J.T.

(2017) Nat Chem Biol 13: 850-857

Released	2017-05-24
Method	X-RAY DIFFRACTION 1.601 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Lysozyme,DCN1-like protein 1 (protein)
Unique Ligands	8ZD

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5V89 \| pdb_00005v89	Download File View File

Structure of DCN4 PONY domain bound to CUL1 WHB

Guy, R.K., Schulman, B.A., Scott, D.C., Hammill, J.T.

(2017) Nat Chem Biol 13: 850-857

Released	2017-05-24
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Cullin-1 (protein) DCN1-like protein 4 (protein)

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6BG3 \| pdb_00006bg3	Download File View File

Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl acetate bound to DCN1

Guy, R.K., Schulman, B.A., Scott, D.C., Hammill, J.T.

(2018) J Med Chem 61: 2680-2693

Released	2018-09-26
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Endolysin, DCN1-like protein 1 chimera (protein)
Unique Ligands	DOJ

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6BG5 \| pdb_00006bg5	Download File View File

Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluoromethyl)phenyl)urea bound to DCN1

Guy, R.K., Schulman, B.A., Scott, D.C., Hammill, J.T.

(2018) J Med Chem 61: 2680-2693

Released	2018-09-26
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Endolysin, DCN1-like protein 1 chimera (protein)
Unique Ligands	DQD

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6P5V \| pdb_00006p5v	Download File View File

Structure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)-3-methylbenzamide

Guy, R.K., Kim, H.S., Hammill, J.T., Scott, D.C., Schulman, B.A.

(2019) J Med Chem 62: 8429-8442

Released	2019-09-11
Method	X-RAY DIFFRACTION 1.398 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Lysozyme,DCN1-like protein 1 fusion (protein)
Unique Ligands	MPD, O37

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6P5W \| pdb_00006p5w	Download File View File

Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)benzamide

Guy, R.K., Kim, H.S., Hammill, J.T., Scott, D.C., Schulman, B.A.

(2019) J Med Chem 62: 8429-8442

Released	2019-09-11
Method	X-RAY DIFFRACTION 1.69 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Lysozyme,DCN1-like protein 1 chimera (protein)
Unique Ligands	O0A