1A7S - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ATOMIC RESOLUTION STRUCTURE OF HBP

Authors :   S. Karlsen, L. F. Iversen, I. K. Larsen, H. J. Flodgaard, J. S. Kastrup

Date :   17 Mar 98 (Deposition) - 23 Mar 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.12

Chains :   Asym./Biol. Unit : A

Keywords :   Serine Protease Homolog, Endotoxin Binding, Heparin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Karlsen, L. F. Iversen, I. K. Larsen, H. J. Flodgaard, J. S. Kastrup
Atomic Resolution Structure Of Human Hbp/Cap37/Azurocidin.
Acta Crystallogr. , Sect. D V. 54 598 1998
PubMed-ID: 9761855 | Reference-DOI: 10.1107/S0907444997016193
(for further references see the PDB file header)

Molecule 1 - HEPARIN BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF-900
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULO VIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Strain	:	ACMNPV
	Synonym	:	CAP37, AZUROCIDIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 19)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EOH	15	Ligand/Ion	ETHANOL
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:10 , SER A:103 , ASN A:114 , HOH A:533 , HOH A:569 , HOH A:668	BINDING SITE FOR RESIDUE NAG A 401
02	AC2	SOFTWARE	ARG A:5 , ARG A:122 , PHE A:143 , ASN A:145 , ASP A:152 , NAG A:412 , HOH A:484	BINDING SITE FOR RESIDUE NAG A 411
03	AC3	SOFTWARE	ASP A:152 , NAG A:411	BINDING SITE FOR RESIDUE NAG A 412
04	AC4	SOFTWARE	LEU A:112	BINDING SITE FOR RESIDUE CL A 450
05	AC5	SOFTWARE	ARG A:10 , GLY A:56 , ALA A:57 , TYR A:58 , SER A:67 , HOH A:485 , HOH A:498 , HOH A:536	BINDING SITE FOR RESIDUE EOH A 417
06	AC6	SOFTWARE	GLY A:22 , EOH A:422 , EOH A:431 , HOH A:693 , HOH A:699	BINDING SITE FOR RESIDUE EOH A 418
07	AC7	SOFTWARE	PHE A:12 , PHE A:14 , GLN A:124 , VAL A:125 , ALA A:126 , PRO A:178 , VAL A:180	BINDING SITE FOR RESIDUE EOH A 419
08	AC8	SOFTWARE	LEU A:208 , EOH A:430 , HOH A:680 , HOH A:754	BINDING SITE FOR RESIDUE EOH A 420
09	AC9	SOFTWARE	ILE A:170 , CYS A:171 , GLY A:175 , SER A:190 , EOH A:424 , HOH A:523 , HOH A:545	BINDING SITE FOR RESIDUE EOH A 421
10	BC1	SOFTWARE	GLN A:19 , THR A:52 , VAL A:54 , THR A:70 , EOH A:418 , EOH A:431 , HOH A:587	BINDING SITE FOR RESIDUE EOH A 422
11	BC2	SOFTWARE	ARG A:132 , ARG A:136 , HOH A:622 , HOH A:741	BINDING SITE FOR RESIDUE EOH A 423
12	BC3	SOFTWARE	CYS A:171 , ASN A:172 , SER A:192 , CYS A:196 , EOH A:421 , EOH A:427	BINDING SITE FOR RESIDUE EOH A 424
13	BC4	SOFTWARE	GLN A:153 , PRO A:200 , PHE A:202 , HOH A:566 , HOH A:669 , HOH A:691	BINDING SITE FOR RESIDUE EOH A 425
14	BC5	SOFTWARE	GLN A:85 , LEU A:87 , ARG A:166	BINDING SITE FOR RESIDUE EOH A 426
15	BC6	SOFTWARE	EOH A:424 , HOH A:552 , HOH A:678 , HOH A:687	BINDING SITE FOR RESIDUE EOH A 427
16	BC7	SOFTWARE	GLN A:69 , THR A:70 , ARG A:97	BINDING SITE FOR RESIDUE EOH A 428
17	BC8	SOFTWARE	GLN A:94 , PRO A:220 , GLY A:221 , HOH A:675	BINDING SITE FOR RESIDUE EOH A 429
18	BC9	SOFTWARE	PRO A:156 , ARG A:205 , EOH A:420 , HOH A:746	BINDING SITE FOR RESIDUE EOH A 430
19	CC1	SOFTWARE	EOH A:418 , EOH A:422	BINDING SITE FOR RESIDUE EOH A 431

Asymmetric/Biological Unit

No.	Residues
1	A:26	-	A:42
2	A:123	-	A:181
3	A:154	-	A:160
4	A:171	-	A:196

Asymmetric/Biological Unit

No.	Residues
1	Gly A:199	-	Pro A:200

(no "SAP(SNP)/Variant" information available for 1A7S)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	CAP7_HUMAN	27-244	1	A:1-218

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENST00000233997	2	ENSE00001236585	chr19:827831-827904	74	CAP7_HUMAN	1-20	20	0	-	-
1.3	ENST00000233997	3	ENSE00001236572	chr19:828230-828386	157	CAP7_HUMAN	20-72	53	1	A:1-43	43
1.4	ENST00000233997	4	ENSE00001236566	chr19:829562-829706	145	CAP7_HUMAN	72-120	49	1	A:48-94	47
1.5a	ENST00000233997	5a	ENSE00001332741	chr19:830708-830941	234	CAP7_HUMAN	121-198	78	1	A:95-172	78
1.5c	ENST00000233997	5c	ENSE00001154873	chr19:831716-832017	302	CAP7_HUMAN	199-251	53	1	A:173-225	53

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:221
 aligned with CAP7_HUMAN | P20160 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:225
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246     
           CAP7_HUMAN    27 IVGGRKARPRQFPFLASIQNQGRHFCGGALIHARFVMTAASCFQSQNPGVSTVVLGAYDLRRRERQSRQTFSISSMSENGYDPQQNLNDLMLLQLDREANLTSSVTILPLPLQNATVEAGTRCQVAGWGSQRSGGRLSRFPRFVNVTVTPEDQCRPNNVCTGVLTRRGGICNGDGGTPLVCEGLAHGVASFSLGPCGRGPDFFTRVALFRDWIDGVLNNPGPGPA 251
               SCOP domains d1a7sa_ A: Heparin binding protein, HBP                                                                                                                                                                                           SCOP domains
               CATH domains 1a7sA01     1a7sA02 A:13-107,A:208-221 Tryp    sin-like serine proteases                                   1a7sA01 A:1-12,A:108-207 Trypsin-like serine proteases                                              1a7sA02       ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee..eeeeeeeeee..eeee.hhh.----...eeeee.............eeeeeeeee.............eeeee..........................eeeeee..............eeeeee...hhh....eeee................eeee..eeeeeeeee........eeeeehhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE TRYPSIN_DOM  PDB: A:1-218 UniProt: 27-244                                                                                                                                                                                 ------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-43 UniProt: 20-72          ------------------------------------------------Exon 1.5a  PDB: A:95-172 UniProt: 121-198                                     Exon 1.5c  PDB: A:173-225 UniProt: 199-251            Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.4  PDB: A:48-94 UniProt: 72-120           ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1a7s A   1 IVGGRKARPRQFPFLASIQNQGRHFCGGALIHARFVMTAASCF----PGVSTVVLGAYDLRRRERQSRQTFSISSMSENGYDPQQNLNDLMLLQLDREANLTSSVTILPLPLQNATVEAGTRCQVAGWGSQRSGGRLSRFPRFVNVTVTPEDQCRPNNVCTGVLTRRGGICNGDGGTPLVCEGLAHGVASFSLGPCGRGPDFFTRVALFRDWIDGVLNNPGPGPA 225
                                    10        20        30        40  |    |50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
                                                                     43   48

Legend:		→ Mismatch	(orange background)
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	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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Heparin binding protein, HBP (4)

Human (Homo sapiens) [TaxId: 9606] (4)

d1a7sa_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Human (Homo sapiens) (615)

1a	1a7sA01	A:1-12,A:108-207
1b	1a7sA02	A:13-107,A:208-221

(no "Pfam Domain" information available for 1A7S)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CAP7_HUMAN | P20160)

molecular function
	GO:0043395	heparan sulfate proteoglycan binding	Interacting selectively and non-covalently with a heparan sulfate proteoglycan, any proteoglycan containing heparan sulfate as the glycosaminoglycan carbohydrate unit.
	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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0015643	toxic substance binding	Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
biological process
	GO:0019730	antimicrobial humoral response	An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus.
	GO:0035584	calcium-mediated signaling using intracellular calcium source	A series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response.
	GO:0060326	cell chemotaxis	The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0045123	cellular extravasation	The migration of a leukocyte from the blood vessels into the surrounding tissue.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0008347	glial cell migration	The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.
	GO:0050930	induction of positive chemotaxis	Any process that initiates the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0048246	macrophage chemotaxis	The movement of a macrophage in response to an external stimulus.
	GO:0001774	microglial cell activation	The change in morphology and behavior of a microglial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
	GO:0042117	monocyte activation	The change in morphology and behavior of a monocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0070944	neutrophil mediated killing of bacterium	The directed killing of a bacterium by a neutrophil.
	GO:0045348	positive regulation of MHC class II biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II.
	GO:0045785	positive regulation of cell adhesion	Any process that activates or increases the frequency, rate or extent of cell adhesion.
	GO:0050754	positive regulation of fractalkine biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fractalkine, a chemokine involved in the control of the key regulatory mechanisms of cell trafficking at sites of inflammation.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0050725	positive regulation of interleukin-1 beta biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-1 beta.
	GO:0010800	positive regulation of peptidyl-threonine phosphorylation	Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
	GO:0050766	positive regulation of phagocytosis	Any process that activates or increases the frequency, rate or extent of phagocytosis.
	GO:0045860	positive regulation of protein kinase activity	Any process that activates or increases the frequency, rate or extent of protein kinase activity.
	GO:0042535	positive regulation of tumor necrosis factor biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
	GO:0070528	protein kinase C signaling	A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
	GO:0007205	protein kinase C-activating G-protein coupled receptor signaling pathway	The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of protein kinase C (PKC). PKC is activated by second messengers including diacylglycerol (DAG).
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0043114	regulation of vascular permeability	Any process that modulates the extent to which blood vessels can be pervaded by fluid.
cellular component
	GO:0042582	azurophil granule	Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
	GO:0035577	azurophil granule membrane	The lipid bilayer surrounding an azurophil granule, a primary lysosomal granule found in neutrophil granulocytes that contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:199 - Pro A:200	[ RasMol ]

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	1a7s
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	CAP7_HUMAN \| P20160	:	1ae5 1fy1 1fy3

(no "Related Entries Specified in the PDB File" available for 1A7S)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (19, 19)

SS Bonds (4, 4)

Cis Peptide Bonds (1, 1)

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SAPs(SNPs)/Variants (0, 0)

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Exons (4, 4)

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