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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "HYDROLASE, PROTEIN BINDING"

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Search Summary

This query matches 107 Structures.

Refinements

Structure Determination Methodology

experimental (107)

Scientific Name of Source Organism

	Homo sapiens (65)
	Bacillus amyloliquefaciens (6)
	Mus musculus (5)
	Schizosaccharomyces pombe 972h- (5)
	Bos taurus (4)
	Rattus norvegicus (4)
	Danio rerio (3)
	Drosophila melanogaster (3)
	Lama glama (3)
	Saccharomyces cerevisiae S288C (3)

More...

Taxonomy

	Eukaryota (88)
	Bacteria (15)
	Riboviria (10)
	Duplodnaviria (3)
	other sequences (3)
	Archaea (2)
	unclassified viruses (2)
	Riboviria (RNA viruses and viroids) (1)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (88)
	ELECTRON MICROSCOPY (19)

Polymer Entity Type

	Protein (107)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (22)
	2.0 - 2.5 (35)
	2.5 - 3.0 (21)
	3.0 - 3.5 (14)
	3.5 - 4.0 (3)
	4.0 - 4.5 (2)
	> 4.5 (4)

Release Date

	2000 - 2004 (5)
	2005 - 2009 (11)
	2010 - 2014 (39)
	2015 - 2019 (35)
	2020 - 2024 (17)

Enzyme Classification Name

	Hydrolases (97)
	Transferases (10)

Membrane Protein Annotation

OPM (3)

Symmetry Type

	Asymmetric (98)
	Cyclic (9)
	Dihedral (3)
	Tetrahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (36)
	Alpha and beta proteins (a/b) (13)
	Artifacts (14)
	All beta proteins (12)
	All alpha proteins (7)
	Small proteins (3)

AllSelected

1 to 25 of 107 Structures

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1IS7 \| pdb_00001is7	Download File View File

Crystal structure of rat GTPCHI/GFRP stimulatory complex

Maita, N., Okada, K., Hatakeyama, K., Hakoshima, T.

(2002) Proc Natl Acad Sci U S A 99: 1212-1217

Released	2002-02-20
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Rattus norvegicus
Macromolecule	GTP Cyclohydrolase I (protein) GTP Cyclohydrolase I Feedback Regulatory Protein (protein)
Unique Ligands	K, PHE

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1IS8 \| pdb_00001is8	Download File View File

Crystal structure of rat GTPCHI/GFRP stimulatory complex plus Zn

Maita, N., Okada, K., Hatakeyama, K., Hakoshima, T.

(2002) Proc Natl Acad Sci U S A 99: 1212-1217

Released	2002-02-20
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Rattus norvegicus
Macromolecule	GTP Cyclohydrolase I (protein) GTP Cyclohydrolase I Feedback Regulatory Protein (protein)
Unique Ligands	K, PHE, ZN

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1TX6 \| pdb_00001tx6	Download File View File

trypsin:BBI complex

Song, H.K., Park, E.Y., Kim, J.A., Kim, H.W., Kim, Y.S.

(2004) J Mol Biology 343: 173-186

Released	2005-03-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hordeum vulgare Sus scrofa
Macromolecule	Bowman-Birk type trypsin inhibitor (protein) Trypsin (protein)
Unique Ligands	CA

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1UPT \| pdb_00001upt	Download File View File

Structure of a complex of the golgin-245 GRIP domain with Arl1

Panic, B., Perisic, O., Veprintsev, D.B., Williams, R.L., Munro, S.

(2003) Mol Cell 12: 863

Released	2003-10-30
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1 (protein) GOLGI AUTOANTIGEN, GOLGIN SUBFAMILY A MEMBER 4 (protein)
Unique Ligands	GTP, MG

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1V5I \| pdb_00001v5i	Download File View File

Crystal structure of serine protease inhibitor POIA1 in complex with subtilisin BPN'

Lee, W.C., Kikkawa, M., Kojima, S., Miura, K., Tanokura, M.

To be published

Released	2005-03-08
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Bacillus amyloliquefaciens Pleurotus ostreatus
Macromolecule	IA-1=serine proteinase inhibitor (protein) Subtilisin BPN' (protein)
Unique Ligands	CA, GOL, SO4

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1WPL \| pdb_00001wpl	Download File View File

Crystal structure of the inhibitory form of rat GTP cyclohydrolase I/GFRP complex

Maita, N., Hatakeyama, K., Okada, K., Hakoshima, T.

(2004) J Biological Chem 279: 51534-51540

Released	2004-09-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Rattus norvegicus
Macromolecule	GTP cyclohydrolase I (protein) GTP cyclohydrolase I feedback regulatory protein (protein)
Unique Ligands	3PO, HBI, NA, ZN

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1X1U \| pdb_00001x1u	Download File View File

Water-mediate interaction at aprotein-protein interface

Ikura, T., Urakubo, Y., Ito, N.

(2004) Chem Phys 307: 111-119

Released	2005-04-26
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus amyloliquefaciens
Macromolecule	Barstar (protein) Ribonuclease (protein)

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1X1W \| pdb_00001x1w	Download File View File

Water-mediate interaction at aprotein-protein interface

Ikura, T., Urakubo, Y., Ito, N.

(2004) Chem Phys 307: 111-119

Released	2005-04-26
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bacillus amyloliquefaciens
Macromolecule	Barstar (protein) Ribonuclease (protein)

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1X1X \| pdb_00001x1x	Download File View File

Water-mediate interaction at aprotein-protein interface

Ikura, T., Urakubo, Y., Ito, N.

(2004) Chem Phys 307: 111-119

Released	2005-04-26
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus amyloliquefaciens
Macromolecule	Barstar (protein) Ribonuclease (protein)

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1X1Y \| pdb_00001x1y	Download File View File

Water-mediate interaction at aprotein-protein interface

Ikura, T., Urakubo, Y., Ito, N.

(2004) Chem Phys 307: 111-119

Released	2005-04-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bacillus amyloliquefaciens
Macromolecule	Barstar (protein) Ribonuclease (protein)

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1ZNV \| pdb_00001znv	Download File View File

How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor

Doudeva, L.G., Huang, H., Hsia, K.C., Shi, Z., Li, C.L., Shen, Y., Yuan, H.S.

(2006) Protein Sci 15: 269-280

Released	2006-03-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Colicin E7 (protein) Colicin E7 immunity protein (protein)
Unique Ligands	NI, PO4

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2G4D \| pdb_00002g4d	Download File View File

Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1

Xu, Z., Chau, S.F., Lam, K.H., Au, S.W.N.

(2006) Biochem J 398: 345-352

Released	2006-10-17
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	SENP1 protein (protein) Small ubiquitin-related modifier 1 (protein)

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2PT7 \| pdb_00002pt7	Download File View File

Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)

Hare, S., Fischer, W., Williams, R., Terradot, L., Bayliss, R., Haas, R., Waksman, G.

(2007) EMBO J 26: 4926-4934

Released	2007-11-13
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Helicobacter pylori 26695
Macromolecule	Cag-alfa (protein) Hypothetical protein (protein)

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2WDT \| pdb_00002wdt	Download File View File

Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME

Weihofen, W.A., Artavanis-Tsakonas, K., Gaudet, R., Ploegh, H.L.

(2010) J Biological Chem 285: 6857

Released	2009-12-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens Plasmodium falciparum
Macromolecule	UBIQUITIN (protein) UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3 (protein)
Unique Ligands	CL

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2XZD \| pdb_00002xzd	Download File View File

Caspase-3 in Complex with an Inhibitory DARPin-3.4

Barandun, J., Schroeder, T., Mittl, P., Grutter, M.G.

(2013) Structure 21: 277

Released	2011-12-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	CASPASE-3 (protein) DARPIN-3.4 (protein)
Unique Ligands	MPD, MRD

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2XZT \| pdb_00002xzt	Download File View File

Caspase-3 in Complex with DARPin-3.4_I78S

Barandun, J., Schroeder, T., Mittl, P., Grutter, M.G.

To be published

Released	2011-12-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	CASPASE-3 (protein) DARPIN-3.4_I78S (protein)
Unique Ligands	MRD

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2Y0B \| pdb_00002y0b	Download File View File

Caspase-3 in Complex with an Inhibitory DARPin-3.4_S76R

Barandun, J., Schroeder, T., Mittl, P., Grutter, M.G.

(2013) Structure 21: 277

Released	2011-12-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	CASPASE-3 (protein) CASPASE-3 SUBUNIT P17 (protein) DARPIN-3.4_S76R (protein)
Unique Ligands	MPD, MRD

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3FQD \| pdb_00003fqd	Download File View File

Crystal Structure of the S. pombe Rat1-Rai1 Complex

Xiang, S., Tong, L.

(2009) Nature 458: 784-788

Released	2009-02-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	5'-3' exoribonuclease 2 (protein) Protein din1 (protein)
Unique Ligands	GOL, MG

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3NHE \| pdb_00003nhe	Download File View File

High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin

Schormann, N., DeLucas, L.J., Powell McCombs, D.

To be published

Released	2010-06-30
Method	X-RAY DIFFRACTION 1.26 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein) Ubiquitin carboxyl-terminal hydrolase 2 (protein)
Unique Ligands	ZN

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3O65 \| pdb_00003o65	Download File View File

Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity

Weeks, S.D., Grasty, K.C., Hernandez-Cuebas, L., Loll, P.J.

(2011) J Biological Chem 286: 4555-4565

Released	2010-11-24
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Putative ataxin-3-like protein (protein) Ubiquitin (protein)
Unique Ligands	NA

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3PHX \| pdb_00003phx	Download File View File

OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15

Akutsu, M., Ye, Y., Virdee, S., Komander, D.

(2011) Proc Natl Acad Sci U S A 108: 2228-2233

Released	2011-02-02
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Crimean-Congo hemorrhagic fever virus strain IbAr10200 Homo sapiens
Macromolecule	RNA-directed RNA polymerase L (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	ACY, NEH, ZN

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3PSE \| pdb_00003pse	Download File View File

Structure of a viral OTU domain protease bound to interferon-stimulated gene 15 (ISG15)

Bacik, J.P., James, T.W., Frias-Staheli, N., Garcia-Sastre, A., Mark, B.L.

(2011) Proc Natl Acad Sci U S A 108: 2222-2227

Released	2011-01-19
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens Orthonairovirus haemorrhagiae
Macromolecule	RNA polymerase (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	4LJ, GOL

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3PT2 \| pdb_00003pt2	Download File View File

Structure of a viral OTU domain protease bound to Ubiquitin

James, T.W., Bacik, J.P., Frias-Staheli, N., Garcia-Sastre, A., Mark, B.L.

(2011) Proc Natl Acad Sci U S A 108: 2222-2227

Released	2011-01-19
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens Orthonairovirus haemorrhagiae
Macromolecule	RNA polymerase (protein) Ubiquitin B (protein)
Unique Ligands	4LJ, ACT, SO4

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3Q3F \| pdb_00003q3f	Download File View File

Engineering Domain-Swapped Binding Interfaces by Mutually Exclusive Folding: Insertion of Ubiquitin into position 103 of Barnase

Ha, J.-H., Karchin, J.M., Walker-Kopp, N., Huang, L.-S., Berry, E.A., Loh, S.N.

(2012) J Mol Biology 416: 495-502

Released	2012-01-25
Method	X-RAY DIFFRACTION 2.169 Å
Organisms	Bacillus amyloliquefaciens Homo sapiens
Macromolecule	Ribonuclease/Ubiquitin chimeric protein (protein)
Unique Ligands	SO4

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3QIS \| pdb_00003qis	Download File View File

Recognition of the F&H motif by the Lowe Syndrome protein OCRL

Pirruccello, M., Swan, L.E., Folta-Stogniew, E., De Camilli, P.

(2011) Nat Struct Mol Biol 18: 789-795

Released	2011-06-15
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Inositol polyphosphate 5-phosphatase OCRL-1 (protein) Protein FAM109A (protein)

1 to 25 of 107 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

1IS7 | pdb_00001is7

1IS8 | pdb_00001is8

1TX6 | pdb_00001tx6

1UPT | pdb_00001upt

1V5I | pdb_00001v5i

1WPL | pdb_00001wpl

1X1U | pdb_00001x1u

1X1W | pdb_00001x1w

1X1X | pdb_00001x1x

1X1Y | pdb_00001x1y

1ZNV | pdb_00001znv

2G4D | pdb_00002g4d

2PT7 | pdb_00002pt7

2WDT | pdb_00002wdt

2XZD | pdb_00002xzd

2XZT | pdb_00002xzt

2Y0B | pdb_00002y0b

3FQD | pdb_00003fqd

3NHE | pdb_00003nhe

3O65 | pdb_00003o65

3PHX | pdb_00003phx

3PSE | pdb_00003pse

3PT2 | pdb_00003pt2

3Q3F | pdb_00003q3f

3QIS | pdb_00003qis