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Title :   CRYSTAL STRUCTURE OF THE PROTHROMBINASE COMPLEX FROM THE VENOM OF PSEUDONAJA TEXTILIS

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

Date :   16 Jul 13 (Deposition) - 31 Jul 13 (Release) - 30 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.71

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

Keywords :   Blood Clotting, Blood Coagulation, Prothrombinase, Factor V, Factor X, Hydrolase, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. C. Lechtenberg, T. A. Murray-Rust, D. J. Johnson, T. E. Adams, S. Krishnaswamy, R. M. Camire, J. A. Huntington
Crystal Structure Of The Prothrombinase Complex From The Venom Of Pseudonaja Textilis.
Blood V. 122 2777 2013
PubMed-ID: 23869089 | Reference-DOI: 10.1182/BLOOD-2013-06-511733

Molecule 1 - FACTOR XA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	STAR
	Expression System Vector	:	PET23
	Expression System Vector Type	:	PLASMID
	Fragment	:	EGF2-CATALYTIC DOMAIN CONSTRUCT, RESIDUES 41-463
	Organ	:	VENOM GLAND
	Organism Common	:	AUSTRALIAN EASTERN BROWN SNAKE
	Organism Scientific	:	PSEUDONAJA TEXTILIS
	Organism Taxid	:	8673
	Other Details	:	PSEUTARIN C CATALYTIC SUBUNIT

Molecule 2 - COAGULATION FACTOR V
	Chains	:	F
	Fragment	:	A2 PEPTIDE, RESIDUES 693-710
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	663 TO 680 OF P. TEXTILIS FV
	Synonym	:	FACTOR V A2 PEPTIDE
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	0GJ	2	Ligand/Ion	L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL]AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE
2	GOL	3	Ligand/Ion	GLYCEROL
3	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:350 , ASP A:351 , ARG A:388 , LYS A:391	BINDING SITE FOR RESIDUE NA A1412
2	AC2	SOFTWARE	CYS B:89 , ARG B:90 , ASP B:92 , ASN B:93 , GLN B:294 , VAL B:295	BINDING SITE FOR RESIDUE GOL B1413
3	AC3	SOFTWARE	ASN B:293 , GLN B:294 , LYS B:298	BINDING SITE FOR RESIDUE GOL B1414
4	AC4	SOFTWARE	TYR A:262 , 0GJ A:1411	BINDING SITE FOR RESIDUE GOL A1413
5	AC5	SOFTWARE	HIS A:211 , TYR A:262 , ASP A:356 , ALA A:357 , CYS A:358 , GLN A:359 , GLY A:360 , SER A:362 , SER A:381 , SER A:382 , GLY A:383 , GLY A:385 , GLY A:393 , GOL A:1413 , HOH A:2063 , HOH A:2081 , HOH A:2086	BINDING SITE FOR LIGAND 0GJ A1411 BOUND TO SER A 362
6	AC6	SOFTWARE	HIS B:211 , TYR B:262 , ASP B:356 , ALA B:357 , CYS B:358 , GLN B:359 , GLY B:360 , SER B:362 , SER B:381 , SER B:382 , GLY B:383 , GLY B:385 , GLY B:393 , HOH B:2019 , HOH B:2062 , HOH B:2063	BINDING SITE FOR LIGAND 0GJ B1412 BOUND TO SER B 362

Asymmetric/Biological Unit

No.	Residues
1	A:89	-	A:100
2	A:96	-	A:109
3	A:111	-	A:124
4	A:132	-	A:285
5	A:176	-	A:181
6	A:196	-	A:212
7	A:333	-	A:347
8	A:358	-	A:386
9	B:89	-	B:100
10	B:96	-	B:109
11	B:111	-	B:124
12	B:132	-	B:285
13	B:176	-	B:181
14	B:196	-	B:212
15	B:333	-	B:347
16	B:358	-	B:386

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

(no "SAP(SNP)/Variant" information available for 4BXW)

(no "PROSITE Motif" information available for 4BXW)

(no "Exon" information available for 4BXW)

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:286
 aligned with Q6IT10_PSETT | Q6IT10 from UniProtKB/TrEMBL  Length:463

    Alignment length:322
                                   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448  
         Q6IT10_PSETT   129 CRVDNGNCWHFCKHVQNDIQCSCAEGYLLGEDGHSCVAGGNFSCGRNIKTRNKREANLPDFVQSQNATLLKKSDNPSPDIRIVNGMDCKLGECPWQAALVDEKEGVFCGGTILSPIYVLTAAHCINETETISVVVGEIDKSRIETGPLLSVDKIYVHKKFVPPQKAYKFDLAAYDYDIAIIQMKTPIQFSENVVPACLPTADFANQVLMKQDFGIVSGFGRIVEKGPKSKTLKVLKVPYVDRHTCMVSSETPITPNMFCAGYDTLPRDACQGDSGGPHTTVYRDTHFITGIVSSGEGCARNGKYGNYTKLSKFIPWIKRIMR 450
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eee.----.eee....eee......eee...........--------------------------------....ee........eeeeee...eeeeeeee....eeeehhhhh......eeee...hhhhhhhh....eeeeeee....hhhhhhhh.........eeeee................hhhhhhhhhhhh.eeeeee..............eeeeee..hhhhhhh.........eeee................eeeeee..eeeeeeeeee..........eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bxw A  89 CRVDNGNCWHFCKH----IQCSCAEGYLLGEDGHSCVAGGNFSCGRNIK--------------------------------IVNGMDCKLGECPWQAALVDEKEGVFCGGTILSPIYVLTAAHCINETETISVVVGEIDKSRIETGPLLSVDKIYVHKKFVPPQKAYKFDLAAYDYDIAIIQMKTPIQFSENVVPACLPTADFANQVLMKQDFGIVSGFGRIVEKGPKSKTLKVLKVPYVDRHTCMVSSETPITPNMFCAGYDTLPRDACQGDSGGPHTTVYRDTHFITGIVSSGEGCARNGKYGNYTKLSKFIPWIKRIMR 410
                                    98   |   108       118       128        |-         -         -         - |     178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408  
                                       102  107                           137                              170

Chain B from PDB  Type:PROTEIN  Length:287
 aligned with Q6IT10_PSETT | Q6IT10 from UniProtKB/TrEMBL  Length:463

    Alignment length:323
                                   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448   
         Q6IT10_PSETT   129 CRVDNGNCWHFCKHVQNDIQCSCAEGYLLGEDGHSCVAGGNFSCGRNIKTRNKREANLPDFVQSQNATLLKKSDNPSPDIRIVNGMDCKLGECPWQAALVDEKEGVFCGGTILSPIYVLTAAHCINETETISVVVGEIDKSRIETGPLLSVDKIYVHKKFVPPQKAYKFDLAAYDYDIAIIQMKTPIQFSENVVPACLPTADFANQVLMKQDFGIVSGFGRIVEKGPKSKTLKVLKVPYVDRHTCMVSSETPITPNMFCAGYDTLPRDACQGDSGGPHTTVYRDTHFITGIVSSGEGCARNGKYGNYTKLSKFIPWIKRIMRQ 451
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eee.----.eee....eee......eee...........--------------------------------....ee........eeeeee...eeeeeeeeee..eeeehhhhh......eeee...hhhhhhhh....eeeeeee....hhhhhhhhh........eeeee................hhhhhhhhhhhh.eeeeee..............eeeeee..hhhhhhhh........eeee................eeeee....eeeeeeeeee.........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bxw B  89 CRVDNGNCWHFCKH----IQCSCAEGYLLGEDGHSCVAGGNFSCGRNIK--------------------------------IVNGMDCKLGECPWQAALVDEKEGVFCGGTILSPIYVLTAAHCINETETISVVVGEIDKSRIETGPLLSVDKIYVHKKFVPPQKAYKFDLAAYDYDIAIIQMKTPIQFSENVVPACLPTADFANQVLMKQDFGIVSGFGRIVEKGPKSKTLKVLKVPYVDRHTCMVSSETPITPNMFCAGYDTLPRDACQGDSGGPHTTVYRDTHFITGIVSSGEGCARNGKYGNYTKLSKFIPWIKRIMRQ 411
                                    98   |   108       118       128        |-         -         -         - |     178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408   
                                       102  107                           137                              170

Chain F from PDB  Type:PROTEIN  Length:8
 aligned with FA5_PSETE | Q593B6 from UniProtKB/Swiss-Prot  Length:1459

    Alignment length:8
            FA5_PSETE   703 DIFADIFI 710
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...eeeee Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4bxw F  11 DIFADIFI  18

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 '\|'

(no "SCOP Domain" information available for 4BXW)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q6IT10_PSETT | Q6IT10)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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: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:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of 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).
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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

Chain F (FA5_PSETE | Q593B6)

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.
	GO:0016504	peptidase activator activity	Binds to and increases the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
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:0010952	positive regulation of peptidase activity	Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins.
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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	Q6IT10_PSETT \| Q6IT10	:	4bxs

4bxs	CRYSTAL STRUCTURE OF THE PROTHROMBINASE COMPLEX FROM THE VENOM OF PSEUDONAJA TEXTILIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (16, 16)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (13, 15)

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Related Entries

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Related Entries Specified in the PDB File