1JMJ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF NATIVE HEPARIN COFACTOR II

Authors :   T. P. Baglin, R. W. Carrell, F. C. Church, J. A. Huntington

Date :   18 Jul 01 (Deposition) - 30 Aug 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym./Biol. Unit : A,B

Keywords :   Serpin, Thrombin Inhibitor, Heparin, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. P. Baglin, R. W. Carrell, F. C. Church, C. T. Esmon, J. A. Huntington
Crystal Structures Of Native And Thrombin-Complexed Heparin Cofactor Ii Reveal A Multistep Allosteric Mechanism.
Proc. Natl. Acad. Sci. Usa V. 99 11079 2002
PubMed-ID: 12169660 | Reference-DOI: 10.1073/PNAS.162232399

Molecule 1 - HEPARIN COFACTOR II
	Chains	:	A, B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HC-II

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CA	1	Ligand/Ion	CALCIUM ION
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:368 , NAG A:482 , HOH A:595 , HOH A:648	BINDING SITE FOR RESIDUE NAG A 481
2	AC2	SOFTWARE	NAG A:481 , BMA A:483	BINDING SITE FOR RESIDUE NAG A 482
3	AC3	SOFTWARE	NAG A:482	BINDING SITE FOR RESIDUE BMA A 483
4	AC4	SOFTWARE	ASN B:312 , ASN B:368	BINDING SITE FOR RESIDUE NAG B 481
5	AC5	SOFTWARE	HIS A:290 , HIS A:292 , HOH A:551 , HOH A:631	BINDING SITE FOR RESIDUE CA A 501

(no "SS Bond" information available for 1JMJ)

(no "Cis Peptide Bond" information available for 1JMJ)

Asymmetric/Biological Unit (7, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051953	S	87	N	HEP2_HUMAN	Polymorphism	34324685	A	S	68	N
2	UniProt	VAR_051954	L	129	V	HEP2_HUMAN	Polymorphism	11542069	A/B	L	110	V
3	UniProt	VAR_007112	R	208	H	HEP2_HUMAN	Disease (THPH10)	5907	A/B	R	189	H
4	UniProt	VAR_011748	K	237	R	HEP2_HUMAN	Polymorphism	1042435	A/B	K	218	R
5	UniProt	VAR_011749	T	442	M	HEP2_HUMAN	Polymorphism	5904	A/B	T	423	M
6	UniProt	VAR_054977	E	447	K	HEP2_HUMAN	Disease (THPH10)	142451096	A/B	E	428	K
7	UniProt	VAR_054978	P	462	L	HEP2_HUMAN	Disease (THPH10)	121912420	A/B	P	443	L

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	HEP2_HUMAN	469-479	2	A:450-460 B:450-460

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000215727	1	ENSE00001320327	chr22:21128167-21128433	267	HEP2_HUMAN	-	0	0	-	-
1.2b	ENST00000215727	2b	ENSE00001299470	chr22:21133585-21134489	905	HEP2_HUMAN	1-297	297	2	A:61-278 (gaps) B:94-278	218 185
1.3	ENST00000215727	3	ENSE00000650952	chr22:21138260-21138533	274	HEP2_HUMAN	297-388	92	2	A:278-369 B:278-369	92 92
1.4	ENST00000215727	4	ENSE00000650953	chr22:21140292-21140436	145	HEP2_HUMAN	388-436	49	2	A:369-417 B:369-417	49 49
1.5b	ENST00000215727	5b	ENSE00000879274	chr22:21141163-21142008	846	HEP2_HUMAN	437-499	63	2	A:418-480 B:418-480	63 63

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
	(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:397
 aligned with HEP2_HUMAN | P05546 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:420
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499
           HEP2_HUMAN    80 LDLEKIFSEDDDYIDIVDSLSVSPTDSDVSAGNILQLFHGKSRIQRLNILNAKFAFNLYRVLKDQVNTFDNIFIAPVGISTAMGMISLGLKGETHEQVHSILHFKDFVNASSKYEITTIHNLFRKLTHRLFRRNFGYTLRSVNDLYIQKQFPILLDFKTKVREYYFAEAQIADFSDPAFISKTNNHIMKLTKGLIKDALENIDPATQMMILNCIYFKGSWVNKFPVEMTHNHNFRLNEREVVKVSMMQTKGNFLAANDQELDCDILQLEYVGGISMLIVVPHKMSGMKTLEAQLTPRVVERWQKSMTNRTREVLLPKFKLEKNYNLVESLKLMGIRMLFDKNGNMAGISDQRIAIDLFKHQGTITVNEEGTQATTVTTVGFMPLSTQVRFTVDRPFLFLIYEHRTSCLLFMGRVANPSRS 499
               SCOP domains d1jmja_ A:                        Heparin cofactor II (Hc-II, leuserpin 2)                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------1jmjA01 A:101-278,A:378-426 Antithrombin, subunit I, domain 2                                                                                                                     1jmjA02 A:279-377,A:427-477 Alpha-1-antitrypsin, domain 1                                          1jmjA01 A:101-278,A:378-426                      1jmjA02 A:279-377,A:427-477                        --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh...-----------------------.......hhhhhhhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.....hhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh................eeeeeeeeee.......hhhhheeeeee.....eeeeeeeeeeeeeeeeee....eeeeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.eeee..eehhhhhhhhh.hhhhh..............eeeeeeeeeeee......................eee....eeeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------N-----------------------------------------V------------------------------------------------------------------------------H----------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M----K--------------L------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     -------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:61-278 (gaps) UniProt: 1-297 [INCOMPLETE]                                                                                                                                                               ------------------------------------------------------------------------------------------Exon 1.4  PDB: A:369-417 UniProt: 388-436        Exon 1.5b  PDB: A:418-480 UniProt: 437-499                      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:278-369 UniProt: 297-388                                                   --------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1jmj A  61 LDLEKIFSEDD-----------------------LQLFHGKSRIQRLNILNAKFAFNLYRVLKDQVNTFDNIFIAPVGISTAMGMISLGLKGETHEQVHSILHFKDFVNASSKYEITTIHNLFRKLTHRLFRRNFGYTLRSVNDLYIQKQFPILLDFKTKVREYYFAEAQIADFSDPAFISKTNNHIMKLTKGLIKDALENIDPATQMMILNCIYFKGSWVNKFPVEMTHNHNFRLNEREVVKVSMMQTKGNFLAANDQELDCDILQLEYVGGISMLIVVPHKMSGMKTLEAQLTPRVVERWQKSMTNRTREVLLPKFKLEKNYNLVESLKLMGIRMLFDKNGNMAGISDQRIAIDLFKHQGTITVNEEGTQATTVTTVGFMPLSTQVRFTVDRPFLFLIYEHRTSCLLFMGRVANPSRS 480
                                    70|        -         -    |  100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480
                                     71                      95

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with HEP2_HUMAN | P05546 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:387
                                   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       402       412       422       432       442       452       462       472       482       492       
           HEP2_HUMAN   113 ILQLFHGKSRIQRLNILNAKFAFNLYRVLKDQVNTFDNIFIAPVGISTAMGMISLGLKGETHEQVHSILHFKDFVNASSKYEITTIHNLFRKLTHRLFRRNFGYTLRSVNDLYIQKQFPILLDFKTKVREYYFAEAQIADFSDPAFISKTNNHIMKLTKGLIKDALENIDPATQMMILNCIYFKGSWVNKFPVEMTHNHNFRLNEREVVKVSMMQTKGNFLAANDQELDCDILQLEYVGGISMLIVVPHKMSGMKTLEAQLTPRVVERWQKSMTNRTREVLLPKFKLEKNYNLVESLKLMGIRMLFDKNGNMAGISDQRIAIDLFKHQGTITVNEEGTQATTVTTVGFMPLSTQVRFTVDRPFLFLIYEHRTSCLLFMGRVANPSRS 499
               SCOP domains d1jmjb_ B: Heparin cofactor II (Hc-II, leuserpin 2)                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------1jmjB01 B:101-278,B:378-426 Antithrombin, subunit I, domain 2                                                                                                                     1jmjB02 B:279-377,B:427-477 Alpha-1-antitrypsin, domain 1                                          1jmjB01 B:101-278,B:378-426                      1jmjB02 B:279-377,B:427-477                        --- CATH domains
           Pfam domains (1) ----------------Serpin-1jmjB01 B:110-477                                                                                                                                                                                                                                                                                                                                                        --- Pfam domains (1)
           Pfam domains (2) ----------------Serpin-1jmjB02 B:110-477                                                                                                                                                                                                                                                                                                                                                        --- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.....hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh................eeeeeeeeee.......hhhhheeeeee.....eeeeeeeeeeeeeeeeee....eeeeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.eeee..eehhhhhhhhh.hhhhh..............eeeeeeeeeeee......................eee....eeeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------V------------------------------------------------------------------------------H----------------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M----K--------------L------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     -------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:94-278 UniProt: 1-297 [INCOMPLETE]                                                                                                                                     ------------------------------------------------------------------------------------------Exon 1.4  PDB: B:369-417 UniProt: 388-436        Exon 1.5b  PDB: B:418-480 UniProt: 437-499                      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: B:278-369 UniProt: 297-388                                                   --------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1jmj B  94 ILQLFHGKSRIQRLNILNAKFAFNLYRVLKDQVNTFDNIFIAPVGISTAMGMISLGLKGETHEQVHSILHFKDFVNASSKYEITTIHNLFRKLTHRLFRRNFGYTLRSVNDLYIQKQFPILLDFKTKVREYYFAEAQIADFSDPAFISKTNNHIMKLTKGLIKDALENIDPATQMMILNCIYFKGSWVNKFPVEMTHNHNFRLNEREVVKVSMMQTKGNFLAANDQELDCDILQLEYVGGISMLIVVPHKMSGMKTLEAQLTPRVVERWQKSMTNRTREVLLPKFKLEKNYNLVESLKLMGIRMLFDKNGNMAGISDQRIAIDLFKHQGTITVNEEGTQATTVTTVGFMPLSTQVRFTVDRPFLFLIYEHRTSCLLFMGRVANPSRS 480
                                   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       383       393       403       413       423       433       443       453       463       473

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Serpins (120)

Superfamily: Serpins (120)

Family: Serpins (100)

Protein domain: Heparin cofactor II (Hc-II, leuserpin 2) (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1jmja_	A:
1b	d1jmjb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Antithrombin; Chain I, domain 2 (100)

Homologous Superfamily: Antithrombin, subunit I, domain 2 (100)

Human (Homo sapiens) (80)

1a	1jmjA01	A:101-278,A:378-426
1b	1jmjB01	B:101-278,B:378-426

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Alpha-1-antitrypsin; domain 1 (101)

Homologous Superfamily: Alpha-1-antitrypsin, domain 1 (101)

Human (Homo sapiens) (81)

2a	1jmjA02	A:279-377,A:427-477
2b	1jmjB02	B:279-377,B:427-477

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Serpin] (63)

Family: Serpin (63)

Homo sapiens (Human) (41)

1a	Serpin-1jmjB01	B:110-477
1b	Serpin-1jmjB02	B:110-477

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HEP2_HUMAN | P05546)

molecular function
	GO:0004866	endopeptidase inhibitor activity	Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
	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: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:0008218	bioluminescence	The production of light by certain enzyme-catalyzed reactions in cells.
	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: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:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	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.
cellular component
	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.

Asymmetric/Biological Unit
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	HEP2_HUMAN \| P05546	:	1jmo 2nat 2ncu 2ncv 2ncw

Description

Compounds

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 13)

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Exons (4, 8)

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