4DY0 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NATIVE PROTEASE NEXIN-1 WITH HEPARIN

Authors :   J. A. Huntington, W. Li

Date :   28 Feb 12 (Deposition) - 15 Aug 12 (Release) - 15 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)
Biol. Unit 4: A (1x),B (1x)

Keywords :   Serpin, Protease Inhibitor, Thrombin, Cell Surface, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Li, J. A. Huntington
Crystal Structures Of Protease Nexin-1 In Complex With Heparin And Thrombin Suggest A 2-Step Recognition Mechanism
Blood V. 120 459 2012
PubMed-ID: 22618708 | Reference-DOI: 10.1182/BLOOD-2012-03-415869

Molecule 1 - GLIA-DERIVED NEXIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SERPINE2, PI7, PN1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GDN, PEPTIDASE INHIBITOR 7, PI-7, PROTEASE NEXIN 1, PN-1, PROTEASE NEXIN I, SERPIN E2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B
Biological Unit 4 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IDS	1	Ligand/Ion	2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3	SGN	1	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	IDS	1	Ligand/Ion	2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3	SGN	1	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	IDS	-1	Ligand/Ion	2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3	SGN	-1	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 8)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IDS	1	Ligand/Ion	2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3	SGN	1	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 4 (4, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	IDS	1	Ligand/Ion	2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3	SGN	1	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:145 , ILE A:146 , ASP A:147 , LYS A:323 , LYS A:325	BINDING SITE FOR RESIDUE SO4 A 401
2	AC2	SOFTWARE	SGN A:403	BINDING SITE FOR RESIDUE IDS A 402
3	AC3	SOFTWARE	LYS A:74 , IDS A:402 , LYS B:74 , LYS B:75 , LYS B:78 , HOH B:600	BINDING SITE FOR RESIDUE SGN A 403
4	AC4	SOFTWARE	LEU A:159 , THR A:160 , LYS A:286 , SER A:318	BINDING SITE FOR RESIDUE GOL A 404
5	AC5	SOFTWARE	GLU A:241 , SER A:242 , LYS B:268 , LYS B:302 , ARG B:346 , HOH B:551	BINDING SITE FOR RESIDUE SO4 B 401
6	AC6	SOFTWARE	LYS A:268 , LYS A:302 , GLU B:241 , SER B:242 , HOH B:654	BINDING SITE FOR RESIDUE SO4 B 402
7	AC7	SOFTWARE	ASN B:148 , LYS B:323 , HOH B:512	BINDING SITE FOR RESIDUE SO4 B 403
8	AC8	SOFTWARE	ARG B:269 , LEU B:343 , ILE B:344 , ALA B:345 , ARG B:346 , PRO B:349	BINDING SITE FOR RESIDUE GOL B 404

(no "SS Bond" information available for 4DY0)

(no "Cis Peptide Bond" information available for 4DY0)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051955	I	51	M	GDN_HUMAN	Polymorphism	3795875	A/B	I	32	M
2	UniProt	VAR_036027	K	204	N	GDN_HUMAN	Unclassified	---	A/B	K	185	N
3	CancerSNP	VAR_GDN_HUMAN_CCDS2460_1_01 *	K	204	N	GDN_HUMAN	Disease (Breast cancer)	---	A/B	K	185	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051955	I	51	M	GDN_HUMAN	Polymorphism	3795875	A	I	32	M
2	UniProt	VAR_036027	K	204	N	GDN_HUMAN	Unclassified	---	A	K	185	N
3	CancerSNP	VAR_GDN_HUMAN_CCDS2460_1_01 *	K	204	N	GDN_HUMAN	Disease (Breast cancer)	---	A	K	185	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051955	I	51	M	GDN_HUMAN	Polymorphism	3795875	B	I	32	M
2	UniProt	VAR_036027	K	204	N	GDN_HUMAN	Unclassified	---	B	K	185	N
3	CancerSNP	VAR_GDN_HUMAN_CCDS2460_1_01 *	K	204	N	GDN_HUMAN	Disease (Breast cancer)	---	B	K	185	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051955	I	51	M	GDN_HUMAN	Polymorphism	3795875	A/B	I	32	M
2	UniProt	VAR_036027	K	204	N	GDN_HUMAN	Unclassified	---	A/B	K	185	N
3	CancerSNP	VAR_GDN_HUMAN_CCDS2460_1_01 *	K	204	N	GDN_HUMAN	Disease (Breast cancer)	---	A/B	K	185	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051955	I	51	M	GDN_HUMAN	Polymorphism	3795875	A/B	I	32	M
2	UniProt	VAR_036027	K	204	N	GDN_HUMAN	Unclassified	---	A/B	K	185	N
3	CancerSNP	VAR_GDN_HUMAN_CCDS2460_1_01 *	K	204	N	GDN_HUMAN	Disease (Breast cancer)	---	A/B	K	185	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	GDN_HUMAN	371-381	2	A:352-362 B:352-362

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	GDN_HUMAN	371-381	1	A:352-362 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	GDN_HUMAN	371-381	1	- B:352-362

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	GDN_HUMAN	371-381	2	A:352-362 B:352-362

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	GDN_HUMAN	371-381	2	A:352-362 B:352-362

(no "Exon" information available for 4DY0)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:362
 aligned with GDN_HUMAN | P07093 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:377
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       
            GDN_HUMAN    22 FNPLSLEELGSNTGIQVFNQIVKSRPHDNIVISPHGIASVLGMLQLGADGRTKKQLAMVMRYGVNGVGKILKKINKAIVSKKNKDIVTVANAVFVKNASEIEVPFVTRNKDVFQCEVRNVNFEDPASACDSINAWVKNETRDMIDNLLSPDLIDGVLTRLVLVNAVYFKGLWKSRFQPENTKKRTFVAADGKSYQVPMLAQLSVFRCGSTSAPNDLWYNFIELPYHGESISMLIALPTESSTPLSAIIPHISTKTIDSWMSIMVPKRVQVILPKFTAVAQTDLKEPLKVLGITDMFDSSKANFAKITTGSENLHVSHILQKAKIEVSEDGTKASAATTAILIARSSPPWFIVDRPFLFFIRHNPTGAVLFMGQINKP 398
               SCOP domains d4dy0a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhhhh........hhhhh......eeeeeeeee........hhhhheeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.....eeeeeeee.....hhhhh....hhhhhhhhhh..eeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh...........---.....eeeeeeeeee.....------------.....eee....eeeeeee....eeeeeeee... Sec.struct. author
             SAPs(SNPs) (1) -----------------------------M--------------------------------------------------------------------------------------------------------------------------------------------------------N-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dy0 A   3 FNPLSLEELGSNTGIQVFNQIVKSRPHDNIVISPHGIASVLGMLQLGADGRTKKQLAMVMRYGVNGVGKILKKINKAIVSKKNKDIVTVANAVFVKNASEIEVPFVTRNKDVFQCEVRNVNFEDPASACDSINAWVKNETRDMIDNLLSPDLIDGVLTRLVLVNAVYFKGLWKSRFQPENTKKRTFVAADGKSYQVPMLAQLSVFRCGSTSAPNDLWYNFIELPYHGESISMLIALPTESSTPLSAIIPHISTKTIDSWMSIMVPKRVQVILPKFTAVAQTDLKEPLKVLGITDMFDSSKANFAKITT---NLHVSHILQKAKIEVSEDGT------------RSSPPWFIVDRPFLFFIRHNPTGAVLFMGQINKP 379
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       | - |     322       332|        -   |   352       362       372       
                                                                                                                                                                                                                                                                                                                                             310 314                333          346

Chain B from PDB  Type:PROTEIN  Length:370
 aligned with GDN_HUMAN | P07093 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:376
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392      
            GDN_HUMAN    23 NPLSLEELGSNTGIQVFNQIVKSRPHDNIVISPHGIASVLGMLQLGADGRTKKQLAMVMRYGVNGVGKILKKINKAIVSKKNKDIVTVANAVFVKNASEIEVPFVTRNKDVFQCEVRNVNFEDPASACDSINAWVKNETRDMIDNLLSPDLIDGVLTRLVLVNAVYFKGLWKSRFQPENTKKRTFVAADGKSYQVPMLAQLSVFRCGSTSAPNDLWYNFIELPYHGESISMLIALPTESSTPLSAIIPHISTKTIDSWMSIMVPKRVQVILPKFTAVAQTDLKEPLKVLGITDMFDSSKANFAKITTGSENLHVSHILQKAKIEVSEDGTKASAATTAILIARSSPPWFIVDRPFLFFIRHNPTGAVLFMGQINKP 398
               SCOP domains d4dy0b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....hhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh........hhhhh......eeeeeeeee........hhhhheeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.....eeeeeeee.....hhhhh....hhhhhhhhhh..eeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh.................eeeeeeeeeeee......------..........eee....eeeeeee....eeeeeeee... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------M--------------------------------------------------------------------------------------------------------------------------------------------------------N-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dy0 B   4 NPLSLEELGSNTGIQVFNQIVKSRPHDNIVISPHGIASVLGMLQLGADGRTKKQLAMVMRYGVNGVGKILKKINKAIVSKKNKDIVTVANAVFVKNASEIEVPFVTRNKDVFQCEVRNVNFEDPASACDSINAWVKNETRDMIDNLLSPDLIDGVLTRLVLVNAVYFKGLWKSRFQPENTKKRTFVAADGKSYQVPMLAQLSVFRCGSTSAPNDLWYNFIELPYHGESISMLIALPTESSTPLSAIIPHISTKTIDSWMSIMVPKRVQVILPKFTAVAQTDLKEPLKVLGITDMFDSSKANFAKITTGSENLHVSHILQKAKIEVSEDGTK------AILIARSSPPWFIVDRPFLFFIRHNPTGAVLFMGQINKP 379
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333|      343       353       363       373      
                                                                                                                                                                                                                                                                                                                                                                    334    341

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Serpins (120)

Superfamily: Serpins (120)

Family: automated matches (20)

Protein domain: automated matches (20)

Human (Homo sapiens) [TaxId: 9606] (9)

1a	d4dy0a_	A:
1b	d4dy0b_	B:

(no "CATH Domain" information available for 4DY0)

(no "Pfam Domain" information available for 4DY0)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GDN_HUMAN | P07093)

molecular function
	GO:0005539	glycosaminoglycan binding	Interacting selectively and non-covalently with any glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0021683	cerebellar granular layer morphogenesis	The process in which the anatomical structure of the cerebellar granular layer is generated and organized. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer.
	GO:0061110	dense core granule biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a dense core granule. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the dense core granule.
	GO:0050974	detection of mechanical stimulus involved in sensory perception	The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception.
	GO:0007566	embryo implantation	Attachment of the blastocyst to the uterine lining.
	GO:0060384	innervation	The process in which a nerve invades a tissue and makes functional synaptic connection within the tissue.
	GO:0060291	long-term synaptic potentiation	A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse.
	GO:0042628	mating plug formation	The deposition of a plug of sperm or other gelatinous material into the opening of the vulva by a male at the termination of copulation. Probably acts to prevent subsequent matings by other males.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0030195	negative regulation of blood coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0014067	negative regulation of phosphatidylinositol 3-kinase signaling	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0010757	negative regulation of plasminogen activation	Any process that decreases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin.
	GO:0010544	negative regulation of platelet activation	Any process that decreases the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue.
	GO:0090331	negative regulation of platelet aggregation	Any process that decreases the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
	GO:0042177	negative regulation of protein catabolic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0010955	negative regulation of protein processing	Any process that decreases the rate, frequency or extent of protein maturation by peptide bond cleavage.
	GO:0045861	negative regulation of proteolysis	Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
	GO:0045879	negative regulation of smoothened signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling.
	GO:0010766	negative regulation of sodium ion transport	Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0048711	positive regulation of astrocyte differentiation	Any process that activates or increases the frequency, rate or extent of astrocyte differentiation.
	GO:0010976	positive regulation of neuron projection development	Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
	GO:0051966	regulation of synaptic transmission, glutamatergic	Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
	GO:0048505	regulation of timing of cell differentiation	The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development.
	GO:0009314	response to radiation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
	GO:0009611	response to wounding	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
	GO:0032940	secretion by cell	The controlled release of a substance by a cell.
	GO:0033363	secretory granule organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion.
	GO:0061108	seminal vesicle epithelium development	The progression of the seminal vesicle epithelium over time, from its formation to the mature structure.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.
	GO:0031232	extrinsic component of external side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its external surface, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031594	neuromuscular junction	The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0031091	platelet alpha granule	A secretory organelle found in blood platelets, which is unique in that it exhibits further compartmentalization and acquires its protein content via two distinct mechanisms: (1) biosynthesis predominantly at the megakaryocyte (MK) level (with some vestigial platelet synthesis) (e.g. platelet factor 4) and (2) endocytosis and pinocytosis at both the MK and circulating platelet levels (e.g. fibrinogen (Fg) and IgG).

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		IDS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SGN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dy0)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4dy0
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GDN_HUMAN \| P07093
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GDN_HUMAN \| P07093
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GDN_HUMAN \| P07093	:	4dy7

(no "Related Entries Specified in the PDB File" available for 4DY0)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (51, 51)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File