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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF BOVINE FACTOR VAI

Authors :   T. E. Adams, M. F. Hockin, K. G. Mann, S. J. Everse

Date :   13 Feb 04 (Deposition) - 29 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Coagulation, Copper-Binding Protein, Cofactor, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. E. Adams, M. F. Hockin, K. G. Mann, S. J. Everse
The Crystal Structure Of Activated Protein C-Inactivated Bovine Factor Va: Implications For Cofactor Function.
Proc. Natl. Acad. Sci. Usa V. 101 8918 2004
PubMed-ID: 15184653 | Reference-DOI: 10.1073/PNAS.0403072101

Molecule 1 - COAGULATION FACTOR V
	Chains	:	A
	Fragment	:	A1 DOMAIN (RESIDUES 29-305)
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	PURIFIED FROM PLASMA
	Synonym	:	ACTIVATED PROTEIN C COFACTOR

Molecule 2 - COAGULATION FACTOR V
	Chains	:	B
	Fragment	:	LIGHT CHAIN (A3, C1, C2 DOMAINS, RESIDUES 1565-2211)
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	PURIFIED FROM PLASMA
	Synonym	:	ACTIVATED PROTEIN C COFACTOR

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CU	1	Ligand/Ion	COPPER (II) ION
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:197 , GLN A:198 , HOH A:2305	BINDING SITE FOR RESIDUE NAG A 2185
2	AC2	SOFTWARE	TYR A:44 , GLN A:46 , VAL A:210 , ASN A:211 , GLN A:289 , ALA A:290 , HOH A:2269	BINDING SITE FOR RESIDUE NAG A 2186
3	AC3	SOFTWARE	PRO B:1661 , ASN B:1662	BINDING SITE FOR RESIDUE NDG B 2187
4	AC4	SOFTWARE	PRO B:1680 , GLY B:1681 , SER B:1682 , ARG B:1711 , TRP B:1784 , ASN B:1811 , GLU B:1832	BINDING SITE FOR RESIDUE NAG B 2188
5	AC5	SOFTWARE	MET B:1721 , ASN B:1969	BINDING SITE FOR RESIDUE NDG B 2189
6	AC6	SOFTWARE	HIS B:1802 , HIS B:1804 , ASP B:1844	BINDING SITE FOR RESIDUE CU B 2190
7	AC7	SOFTWARE	LYS A:93 , GLU A:108 , ASP A:111 , ASP A:112	BINDING SITE FOR RESIDUE CA A 2184

Asymmetric/Biological Unit

No.	Residues
1	A:139	-	A:165
2	B:1684	-	B:1710
3	B:1866	-	B:2020
4	B:2025	-	B:2180

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

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

Asymmetric/Biological Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTICOPPER_OXIDASE1	PS00079	Multicopper oxidases signature 1.	FA5_BOVIN	304-324 1867-1887	2	A:276-296 B:1839-1859
2	FA58C_3	PS50022	Coagulation factors 5/8 type C domain (FA58C) profile.	FA5_BOVIN	1894-2048 2053-2208	2	B:1866-2020 B:2025-2180
3	FA58C_1	PS01285	Coagulation factors 5/8 type C domain (FA58C) signature 1.	FA5_BOVIN	1934-1967 2098-2127	2	B:1906-1939 B:2070-2099
4	FA58C_2	PS01286	Coagulation factors 5/8 type C domain (FA58C) signature 2.	FA5_BOVIN	2032-2048 2192-2208	2	B:2004-2020 B:2164-2180

(no "Exon" information available for 1SDD)

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:268
 aligned with FA5_BOVIN | Q28107 from UniProtKB/Swiss-Prot  Length:2211

    Alignment length:296
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318      
           FA5_BOVIN     29 AKLRQFYVAAQSIRWNYRPESTHLSSKPFETSFKKIVYREYEAYFQKEKPQSRTSGLLGPTLYAEVGDIMKVHFKNKAHKPLSIHAQGIKYSKFSEGASYSDHTLPMEKMDDAVAPGQEYTYEWIISEHSGPTHDDPPCLTHIYYSYVNLVEDFNSGLIGPLLICKKGTLTEDGTQKMFEKQHVLMFAVFDESKSWNQTSSLMYTVNGYVNGTMPDITVCAHDHISWHLIGMSSGPELFSIHFNGQVLEQNHHKISAITLVSATSTTANMTVSPEGRWTIASLIPRHFQAGMQAYI  324
               SCOP domains d1sdda1 A:1-180               Coagulation factor V                                                                                                                                  d1sdda2 A:181-296 Coagulation factor V                                                                               SCOP domains
               CATH domains 1sddA01 A:1-181               Cupredoxins -  blue copper proteins                                                                                                                    1sddA02 A:182-296 Cupredoxins -  blue co      pper proteins                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..eeeeeee.--------------..eeeeeee......................eeee...eeeeeeee........eee.................hhhhhh........eeeeeee.hhhhh.......eeeeeee....hhhhhhh...eeeeee.......................eee..........eee.................------..........ee.........ee..ee.....ee......--------...........hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1  PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1sdd A    1 AKLRQFYVAAQSIRWN--------------TSFKKIVYREYEAYFQKEKPQSRTSGLLGPTLYAEVGDIMKVHFKNKAHKPLSIHAQGIKYSKFSEGASYSDHTLPMEKMDDAVAPGQEYTYEWIISEHSGPTHDDPPCLTHIYYSYVNLVEDFNSGLIGPLLICKKGTLTEDGTQKMFEKQHVLMFAVFDESKSWNQTSSLMYTVNGYVNGTMPDITVCA------HLIGMSSGPELFSIHFNGQVLEQNHHKISAITLVSATSTT--------GRWTIASLIPRHFQAGMQAYI  296
                                    10     |   -         -|       40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220|      230       240       250       260      |  -     | 280       290      
                                          16             31                                                                                                                                                                                           221    228                                    267      276

Chain B from PDB  Type:PROTEIN  Length:601
 aligned with FA5_BOVIN | Q28107 from UniProtKB/Swiss-Prot  Length:2211

    Alignment length:645
                                  1575      1585      1595      1605      1615      1625      1635      1645      1655      1665      1675      1685      1695      1705      1715      1725      1735      1745      1755      1765      1775      1785      1795      1805      1815      1825      1835      1845      1855      1865      1875      1885      1895      1905      1915      1925      1935      1945      1955      1965      1975      1985      1995      2005      2015      2025      2035      2045      2055      2065      2075      2085      2095      2105      2115      2125      2135      2145      2155      2165      2175      2185      2195      2205     
           FA5_BOVIN   1566 NTGNRKYYYIAAEEISWDYSKFVQSDDVDYVPEDTVYKKVVFRKYLDSTFTKLDPQGEYEEHLGILGPVIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEWFKEDNAIQPNKTYTYVWHATTRSGPENPGSACRAWAYYSAVNPEKDIHSGLIGPLLICRKGTLDKETNMPVDMREFVLLFMVFDEKKSWYYDKKPTRSWRRASSEVKNSHEFHAINGMIYNLPGLRMYEQEWVRLHLLNLGGSRDIHVVHFHGQTLLENGTQQHQLGVWPLLPGSFKTLEMKASKPGWWLLDTEVGEIQRAGMQTPFLIVDRECKMPMGLSTGLIADSQIQASEFWGYWEPKLARLNNGGSYNAWIAEKLSTEFNPEPWIQVDMQKEVLLTGIQTQGAKHYLKPYYTTEFCVAYSLDRKNWRIFKGNSTRNVMYFGGNSDASTIKENQIDPPVVARYIRISPTGSYNKPALRLELQGCEVNGCSTPLGMESGKIENKQITASSFKKSWWGNYWEPFLARLNAQGRVNAWQAKANNNNQWLQIDLLKIKKITAIVTQGCKSLSSEMYVKSYTIHYSDQGTDWKPYREKSSMVDKIFEGNNNVRGHVKNFFNPPIISRFIRIIPKTWNQSIALRLELFGCDM 2210
               SCOP domains -----------------------        -------------------------------------------------------------------                     d1sddb1 B:1657-1723 Coagulation factor V                           d1sddb2 B:1724-1862 C               oagulation factor V                                                                                    d1sddb3 B:1863-2024 C2 domain of factor V                                                                                                                         d1sddb4 B:2025-2182 C2 domain of factor V                                                                                                                      SCOP domains
               CATH domains 1sddB01 B:1538-1722 Cup        redoxins -  blue copper proteins                                                                                                                          1sddB02 B:1723-1862 Cu               predoxins -  blue copper proteins                                                                      1sddB03 B:1863-2023 Galactose-binding domain-like                                                                                                                1sddB04 B:2024-2182 Galactose-binding domain-like                                                                                                               CATH domains
           Pfam domains (1) -----------------------        ------------------------------Cu-oxidase_3-1sddB01 B:1599-1713                                                                                   -------------------------------               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_type_C-1sddB03 B:2040-2177                                                                                                          ----- Pfam domains (1)
           Pfam domains (2) -----------------------        ------------------------------Cu-oxidase_3-1sddB02 B:1599-1713                                                                                   -------------------------------               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_type_C-1sddB04 B:2040-2177                                                                                                          ----- Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeeeeee.....--------....eeeeeeeeee..............hhhhh.....eeee...eeeeee..........eee...---------------------........ee..ee.............eeeeeee...hhhhhhh...eeeeeee................eeeeeeeeee.hhh....---------------...eeeee..........eee...eeeeeeee.......eeeee....eee.....eee..eee...eeeeeeee....eeeeee..hhhhhh...eeeeeee.....ee........hhh.eee.......hhhhh..........ee.............eeeeeeeeeeeeeeeee.ee....eeeeeeeeeeee......ee...........ee........eeeeeeeeeeeeeeeeeeeeee...eeeeeeeee....................eee....ee...ee.hhhhh..........ee.........eeeeeeeeeeeeeeeee.eee..eeeeeeee.eeee......ee...........ee........eeeeeeeeeeeeeeee...eee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 ------FA58C_3  PDB: B:1866-2020 UniProt: 1894-2048                                                                                                               ----FA58C_3  PDB: B:2025-2180 UniProt: 2053-2208                                                                                                                -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FA58C_1  PDB: B:1906-1939         ----------------------------------------------------------------FA58C_2          -------------------------------------------------FA58C_1  PDB: B:2070-2099     ----------------------------------------------------------------FA58C_2          -- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1sdd B 1538 NTGNRKYYYIAAEEISWDYSKFV--------PEDTVYKKVVFRKYLDSTFTKLDPQGEYEEHLGILGPVIRAEVDDVIQVRFKNLASRPYSLHAHGLS---------------------NAIQPNKTYTYVWHATTRSGPENPGSACRAWAYYSAVNPEKDIHSGLIGPLLICRKGTLDKETNMPVDMREFVLLFMVFDEKKSWYYD---------------NSHEFHAINGMIYNLPGLRMYEQEWVRLHLLNLGGSRDIHVVHFHGQTLLENGTQQHQLGVWPLLPGSFKTLEMKASKPGWWLLDTEVGEIQRAGMQTPFLIVDRECKMPMGLSTGLIADSQIQASEFWGYWEPKLARLNNGGSYNAWIAEKLSTEFNPEPWIQVDMQKEVLLTGIQTQGAKHYLKPYYTTEFCVAYSLDRKNWRIFKGNSTRNVMYFGGNSDASTIKENQIDPPVVARYIRISPTGSYNKPALRLELQGCEVNGCSTPLGMESGKIENKQITASSFKKSWWGNYWEPFLARLNAQGRVNAWQAKANNNNQWLQIDLLKIKKITAIVTQGCKSLSSEMYVKSYTIHYSDQGTDWKPYREKSSMVDKIFEGNNNVRGHVKNFFNPPIISRFIRIIPKTWNQSIALRLELFGCDM 2182
                                  1547      1557  |      - |    1577      1587      1597      1607      1617      1627       | -         -      1657      1667      1677      1687      1697      1707      1717      1727      1737      |  -         -  |   1767      1777      1787      1797      1807      1817      1827      1837      1847      1857      1867      1877      1887      1897      1907      1917      1927      1937      1947      1957      1967      1977      1987      1997      2007      2017      2027      2037      2047      2057      2067      2077      2087      2097      2107      2117      2127      2137      2147      2157      2167      2177     
                                               1560     1569                                                              1635                  1657                                                                                   1744            1760

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: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Multidomain cupredoxins (146)

Protein domain: Coagulation factor V (1)

Cow (Bos taurus) [TaxId: 9913] (1)

1a	d1sdda1	A:1-180
1b	d1sdda2	A:181-296
1c	d1sddb1	B:1657-1723
1d	d1sddb2	B:1724-1862

Fold: Galactose-binding domain-like (314)

Superfamily: Galactose-binding domain-like (314)

Family: Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) (17)

Protein domain: C2 domain of factor V (4)

Cow (Bos taurus) [TaxId: 9913] (1)

2a	d1sddb3	B:1863-2024
2b	d1sddb4	B:2025-2182

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Cattle (Bos taurus) (16)

1a	1sddB01	B:1538-1722
1b	1sddA01	A:1-181
1c	1sddB02	B:1723-1862
1d	1sddA02	A:182-296

Topology: Jelly Rolls (1293)

Homologous Superfamily: Galactose-binding domain-like (195)

Cattle (Bos taurus) (3)

2a	1sddB03	B:1863-2023
2b	1sddB04	B:2024-2182

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu-oxidase_3 (79)

Bos taurus (Bovine) (1)

1a	Cu-oxidase_3-1sddB01	B:1599-1713
1b	Cu-oxidase_3-1sddB02	B:1599-1713

Clan: GBD (153)

Family: F5_F8_type_C (45)

Bos taurus (Bovine) (2)

2a	F5_F8_type_C-1sddB03	B:2040-2177
2b	F5_F8_type_C-1sddB04	B:2040-2177

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FA5_BOVIN | Q28107)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
cellular component
	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.

Asymmetric/Biological Unit
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	1sdd
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Description

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Ligands, Modified Residues, Ions (4, 7)

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SS Bonds (4, 4)

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