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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/HYDROLASE INHIBITOR/DNA"

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Search Summary

This query matches 10 Structures.

Refinements

Structure Determination Methodology

experimental (10)

Scientific Name of Source Organism

	Homo sapiens (9)
	synthetic construct (4)
	Neisseria meningitidis 8013 (1)

Taxonomy

	Eukaryota (9)
	other sequences (4)
	Bacteria (1)

Experimental Method

X-RAY DIFFRACTION (10)

Polymer Entity Type

	DNA (10)
	Protein (10)
	RNA (1)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (3)
	2.5 - 3.0 (4)
	3.0 - 3.5 (1)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (2)
	2010 - 2014 (6)
	2015 - 2019 (1)

Enzyme Classification Name

Hydrolases (10)

Symmetry Type

Asymmetric (10)

SCOP Classification

All beta proteins (3)

AllSelected

1 to 10 of 10 Structures

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1HAO \| pdb_00001hao	Download File View File

COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTTGGTGTGGTTGG (BASED ON NMR MODEL OF DNA)

Tulinsky, A., Padmanabhan, K.

(1996) Acta Crystallogr D Biol Crystallogr 52: 272-282

Released	1996-04-03
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	ALPHA-THROMBIN heavy chain (protein) ALPHA-THROMBIN light chain (protein) DNA 5'-D(GPGPTPTPGPGPTPGPTPGPGPTPTPGP*G)-3' (nucleic acid)
Unique Ligands	0G6

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1HAP \| pdb_00001hap	Download File View File

COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTTGGTGTGGTTGG (BASED ON X-RAY MODEL OF DNA)

Padmanabhan, K., Tulinsky, A.

(1996) Acta Crystallogr D Biol Crystallogr 52: 272-282

Released	1996-04-03
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Thrombin heavy chain (protein) Thrombin light chain (protein) 5'-D(GPGPTPTPGPGPTPGPTPGPGPTPTPGP*G)-3' (nucleic acid)
Unique Ligands	0G6

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1HUT \| pdb_00001hut	Download File View File

THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER

Padmanabhan, K., Padmanabhan, K.P., Ferrara, J.D., Sadler, J.E., Tulinsky, A.

(1993) J Biological Chem 268: 17651-17654

Released	1994-06-22
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	ALPHA-Thrombin heavy chain (protein) ALPHA-Thrombin light chain (protein) DNA 5'-D(GPGPTPTPGPGPTPGPTPGPGPTPTPGP*G)-3' (nucleic acid)
Unique Ligands	0G7

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3QLP \| pdb_00003qlp	Download File View File

X-ray structure of the complex between human alpha thrombin and a modified thrombin binding aptamer (mTBA)

Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

(2011) Nucleic Acids Res 39: 7858-7867

Released	2011-10-19
Method	X-RAY DIFFRACTION 2.14 Å
Organisms	Homo sapiens
Macromolecule	Thrombin heavy chain (protein) Thrombin light chain (protein) modified thrombin binding DNA aptamer (nucleic acid)
Unique Ligands	0G6, K, NA, NAG

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4DIH \| pdb_00004dih	Download File View File

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of sodium ions

Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

(2012) Nucleic Acids Res 40: 8119-8128

Released	2012-07-18
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Prothrombin (protein) Thrombin binding aptamer (nucleic acid)
Unique Ligands	0G6, CL, NA, NAG, ZN

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4DII \| pdb_00004dii	Download File View File

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions

Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

(2012) Nucleic Acids Res 40: 8119-8128

Released	2012-07-18
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Prothrombin (protein) Thrombin binding aptamer (nucleic acid)
Unique Ligands	0G6, CL, K, NA, NAG, ZN

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4I7Y \| pdb_00004i7y	Download File View File

Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II

Pica, A., Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2403-2411

Released	2013-10-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Prothrombin (protein) DNA (27-MER) (nucleic acid)
Unique Ligands	0G6, NA, NAG

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4LZ1 \| pdb_00004lz1	Download File View File

X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 12 nucleobase

Pica, A., Russo Krauss, I., Merlino, A., Sica, F.

(2013) FEBS J 280: 6581-6588

Released	2014-01-08
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Thrombin heavy chain (protein) Thrombin light chain (protein) Thrombin Binding Aptamer (nucleic acid)
Unique Ligands	0G6, K, NA, NAG

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4LZ4 \| pdb_00004lz4	Download File View File

X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 3 nucleobase

Pica, A., Russo Krauss, I., Merlino, A., Sica, F.

(2013) FEBS J 280: 6581-6588

Released	2014-01-08
Method	X-RAY DIFFRACTION 2.56 Å
Organisms	Homo sapiens
Macromolecule	Thrombin heavy chain (protein) Thrombin light chain (protein) Thrombin Binding Aptamer (TBA) (nucleic acid)
Unique Ligands	0G6, K, NA, NAG

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6JE4 \| pdb_00006je4	Download File View File

Crystal structure of Nme1Cas9-sgRNA-dsDNA dimer mediated by double protein inhibitor AcrIIC3 monomers

Sun, W., Yang, J., Cheng, Z., Liu, C., Wang, K., Huang, X., Wang, Y.

(2019) Mol Cell 76: 938

Released	2019-11-06
Method	X-RAY DIFFRACTION 3.069 Å
Organisms	Neisseria meningitidis 8013 synthetic construct
Macromolecule	AcrIIC3 (protein) CRISPR-associated endonuclease Cas9 (protein) non-target DNA strand (nucleic acid) sgRNA (nucleic acid) target DNA strand (nucleic acid)
Unique Ligands	EDO, PEG

1 to 10 of 10 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1HAO | pdb_00001hao

COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTTGGTGTGGTTGG (BASED ON NMR MODEL OF DNA)

1HAP | pdb_00001hap

COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE GGTTGGTGTGGTTGG (BASED ON X-RAY MODEL OF DNA)

1HUT | pdb_00001hut

THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER

3QLP | pdb_00003qlp

X-ray structure of the complex between human alpha thrombin and a modified thrombin binding aptamer (mTBA)

4DIH | pdb_00004dih

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of sodium ions

4DII | pdb_00004dii

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions

4I7Y | pdb_00004i7y

Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II

4LZ1 | pdb_00004lz1

X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 12 nucleobase

4LZ4 | pdb_00004lz4

X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 3 nucleobase

6JE4 | pdb_00006je4

Crystal structure of Nme1Cas9-sgRNA-dsDNA dimer mediated by double protein inhibitor AcrIIC3 monomers

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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

1HAO | pdb_00001hao

1HAP | pdb_00001hap

1HUT | pdb_00001hut

3QLP | pdb_00003qlp

4DIH | pdb_00004dih

4DII | pdb_00004dii

4I7Y | pdb_00004i7y

4LZ1 | pdb_00004lz1

4LZ4 | pdb_00004lz4

6JE4 | pdb_00006je4