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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: BIRD ID(s) = PRD_000288

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Search Summary

This query matches 16 Structures.

Refinements

Structure Determination Methodology

experimental (16)

Scientific Name of Source Organism

	Homo sapiens (12)
	Desmodus rotundus (1)
	Escherichia coli (1)
	Mus musculus (1)
	Pseudonaja textilis (1)
	Staphylococcus phage 42D.m (1)
	Trimeresurus stejnegeri (1)
	Vicugna pacos (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (16)
	Bacteria (1)
	Duplodnaviria (1)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (16)

Polymer Entity Type

Protein (16)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (2)
	2.0 - 2.5 (1)
	2.5 - 3.0 (10)
	3.0 - 3.5 (2)

Release Date

	1995 - 1999 (4)
	2000 - 2004 (1)
	2005 - 2009 (1)
	2010 - 2014 (1)
	2015 - 2019 (5)
	2020 - 2024 (4)

Enzyme Classification Name

Hydrolases (16)

Symmetry Type

	Asymmetric (14)
	Dihedral (2)
	Cyclic (1)

SCOP Classification

	All beta proteins (13)
	Small proteins (6)
	Alpha and beta proteins (a+b) (1)
	Artifacts (1)

AllSelected

1 to 16 of 16 Structures

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1A5I \| pdb_00001a5i	Download File View File

CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE)

Renatus, M., Stubbs, M.T., Bode, W.

(1997) Biochemistry 36: 13483-13493

Released	1999-03-23
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Desmodus rotundus
Macromolecule	PLASMINOGEN ACTIVATOR (protein)
Unique Ligands	0GJ

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1BQY \| pdb_00001bqy	Download File View File

Plasminogen activator (TSV-PA) from snake venom

Parry, M.A.A., Bode, W.

(1998) Structure 6: 1195-1206

Released	1999-08-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Trimeresurus stejnegeri
Macromolecule	PLASMINOGEN ACTIVATOR (protein)
Unique Ligands	0GJ

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1BUI \| pdb_00001bui	Download File View File

Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action

Parry, M.A.A., Fernandez-Catalan, C., Bergner, A., Huber, R., Hopfner, K., Schlott, B., Guehrs, K., Bode, W.

(1998) Nat Struct Biol 5: 917-923

Released	1999-09-02
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens Staphylococcus phage 42D.m
Macromolecule	Plasminogen (protein) Staphylokinase (protein)
Unique Ligands	0GJ

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1DX5 \| pdb_00001dx5	Download File View File

Crystal structure of the thrombin-thrombomodulin complex

Fuentes-Prior, P., Iwanaga, Y., Huber, R., Pagila, R., Rumennik, G., Seto, M., Morser, J., Light, D.R., Bode, W.

(2000) Nature 404: 518

Released	2000-04-10
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Thrombin heavy chain (protein) Thrombin light chain (protein) Thrombomodulin (protein)
Unique Ligands	0GJ, CA, FMT, NA, NAG

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1LMW \| pdb_00001lmw	Download File View File

LMW U-PA Structure complexed with EGRCMK (GLU-GLY-ARG Chloromethyl Ketone)

Spraggon, G.S., Phillips, C., Nowak, U.K., Ponting, C.P., Saunders, D., Dobson, C.M., Stuart, D.I., Jones, E.Y.

(1995) Structure 3: 681-691

Released	1996-01-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	UROKINASE-TYPE PLASMINOGEN ACTIVATOR (protein)
Unique Ligands	0GJ

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2B8O \| pdb_00002b8o	Download File View File

Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor VIIa/Soluble Tissue Factor Complex

Bajaj, S.P., Schmidt, A.E., Padmanabhan, K.

To be published

Released	2007-02-13
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor VII heavy chain (protein) Coagulation factor VII light chain (protein) Tissue factor (protein)
Unique Ligands	0GJ, CA, CL, FUC, GLC, MG, NA, ZN

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4BXW \| pdb_00004bxw	Download File View File

Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis

Lechtenberg, B.C., Murray-Rust, T.A., Johnson, D.J.D., Adams, T.E., Krishnaswamy, S., Camire, R.M., Huntington, J.A.

(2013) Blood 122: 2777

Released	2013-07-31
Method	X-RAY DIFFRACTION 2.71 Å
Organisms	Escherichia coli Pseudonaja textilis
Macromolecule	COAGULATION FACTOR V (protein) FACTOR XA (protein)
Unique Ligands	0GJ, GOL, NA

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5JB8 \| pdb_00005jb8	Download File View File

Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone

Kristensen, L.H., Brandstetter, H.

(2016) Biochem J 473: 2395-2411

Released	2016-06-01
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor IX (protein)
Unique Ligands	0GJ, CA, DMS

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5JBB \| pdb_00005jbb	Download File View File

Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with EGR-chloromethylketone

Kristensen, L.H., Brandstetter, H.

(2016) Biochem J 473: 2395-2411

Released	2016-06-01
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor IX (protein)
Unique Ligands	0GJ, CA, DMS

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5LHQ \| pdb_00005lhq	Download File View File

The EGR-cmk active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody Nb7

Kromann-Hansen, T., Lange, E.L., Sorensen, H.P., Ghassabeh, G.H., Huang, M., Jensen, J.K., Muyldermans, S., Declerck, P.J., Andreasen, P.A.

(2017) Sci Rep 7: 3385-3385

Released	2017-06-28
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mus musculus Vicugna pacos
Macromolecule	Camelid-Derived Antibody Fragment Nb7 (protein) Urokinase-type plasminogen activator (protein)
Unique Ligands	0GJ, EDO, SO4

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5WI6 \| pdb_00005wi6	Download File View File

Human beta-1 tryptase mutant Ile99Cys

Eigenbrot, C., Maun, H.R.

(2018) J Biological Chem 293: 9614-9628

Released	2018-04-25
Method	X-RAY DIFFRACTION 2.72 Å
Organisms	Homo sapiens
Macromolecule	Tryptase alpha/beta-1 (protein)
Unique Ligands	0GJ, SO4

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6RFK \| pdb_00006rfk	Download File View File

Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant)

Huntington, J.A., Sendall, T.J.

To be published

Released	2019-06-12
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Coagulation factor IX (protein) GLU-GLY-AR7-0QE (protein)
Unique Ligands	B3P, CA, GOL

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6VVU \| pdb_00006vvu	Download File View File

Anti-Tryptase fab E104.v1 bound to tryptase

Ultsch, M., Koerber, J.T.

(2020) Nat Commun 11: 6435-6435

Released	2020-12-30
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Fab E104.v1 heavy chain (protein) Fab E104.v1 light chain (protein) Tryptase alpha/beta-1 (protein)
Unique Ligands	0GJ, CA

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7AHU \| pdb_00007ahu	Download File View File

Anti-FX Fab of mim8 in complex with human FXa

Johansson, E.

(2021) Blood 138: 1258-1268

Released	2021-07-07
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Anti-FX Fab of mim8 heavy chain (protein) Anti-FX Fab of mim8 light chain (protein) Coagulation factor X (protein)
Unique Ligands	0GJ, CA

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7AHV \| pdb_00007ahv	Download File View File

Anti-FIXa Fab of mim8 in complex with human FIXa

Johansson, E.

(2021) Blood 138: 1258-1268

Released	2021-07-07
Method	X-RAY DIFFRACTION 3.11 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor IX (protein) anti-FIXa Fab of mim8 heavy chain (protein) anti-FIXa Fab of mim8 light chain (protein)
Unique Ligands	0GJ, CA, SO4

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8OL9 \| pdb_00008ol9	Download File View File

Anti-FIXa Fab in complex with human des-(Gla-EGF1) FIXa

Johansson, E., Svensson, L.A.

(2023) Protein Sci 32: e4726-e4726

Released	2023-07-19
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Coagulation factor IX heavy chain (protein) Coagulation factor IX light chain (protein) Heavy chain of FIXa binding Fab (protein) Light chain of FIXa binding Fab (protein)
Unique Ligands	0GJ, CA, SO4, TRS

1 to 16 of 16 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.

1A5I | pdb_00001a5i

CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE)

1BQY | pdb_00001bqy

Plasminogen activator (TSV-PA) from snake venom

1BUI | pdb_00001bui

Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action

1DX5 | pdb_00001dx5

Crystal structure of the thrombin-thrombomodulin complex

1LMW | pdb_00001lmw

LMW U-PA Structure complexed with EGRCMK (GLU-GLY-ARG Chloromethyl Ketone)

2B8O | pdb_00002b8o

Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor VIIa/Soluble Tissue Factor Complex

4BXW | pdb_00004bxw

Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis

5JB8 | pdb_00005jb8

Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone

5JBB | pdb_00005jbb

Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with EGR-chloromethylketone

5LHQ | pdb_00005lhq

The EGR-cmk active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody Nb7

5WI6 | pdb_00005wi6

Human beta-1 tryptase mutant Ile99Cys

6RFK | pdb_00006rfk

Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant)

6VVU | pdb_00006vvu

Anti-Tryptase fab E104.v1 bound to tryptase

7AHU | pdb_00007ahu

Anti-FX Fab of mim8 in complex with human FXa

7AHV | pdb_00007ahv

Anti-FIXa Fab of mim8 in complex with human FIXa

8OL9 | pdb_00008ol9

Anti-FIXa Fab in complex with human des-(Gla-EGF1) FIXa

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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

1A5I | pdb_00001a5i

1BQY | pdb_00001bqy

1BUI | pdb_00001bui

1DX5 | pdb_00001dx5

1LMW | pdb_00001lmw

2B8O | pdb_00002b8o

4BXW | pdb_00004bxw

5JB8 | pdb_00005jb8

5JBB | pdb_00005jbb

5LHQ | pdb_00005lhq

5WI6 | pdb_00005wi6

6RFK | pdb_00006rfk

6VVU | pdb_00006vvu

7AHU | pdb_00007ahu

7AHV | pdb_00007ahv

8OL9 | pdb_00008ol9