1X7A - JenaLib

Title :   PORCINE FACTOR IXA COMPLEXED TO 1-{3-[AMINO(IMINO) METHYL]PHENYL}-N-[4-(1H-BENZIMIDAZOL-1-YL)-2-FLUOROPHENYL]-3-(TRIFLUOROMETHYL)-1H-PYRAZOLE-5-CARBOXAMIDE

Authors :   R. S. Alexander, A. M. Smallwood, J. M. Smallheer, J. Wang, S. Wang, S. Nakajima, K. A. Rossi, F. Barbera, D. Burdick, J. M. Luettgen

Date :   13 Aug 04 (Deposition) - 16 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : C,L
Biol. Unit 1: C,L  (1x)
Biol. Unit 2: C,L  (2x)

Keywords :   Inhibition; X-Ray Structure, Blood Clotting, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Smallheer, R. S. Alexander, J. Wang, S. Wang, S. Nakajima, K. A. Rossi, A. Smallwood, F. Barbera, D. Burdick, J. M. Luettgen, R. M. Knabb, R. R. Wexler, P. K. Jadhav
Sar And Factor Ixa Crystal Structure Of A Dual Inhibitor Of Factors Ixa And Xa
Bioorg. Med. Chem. Lett. V. 14 5263 2004
PubMed-ID: 15454208 | Reference-DOI: 10.1016/J.BMCL.2004.08.034
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (9, 9)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (6, 6)

Asymmetric Unit (6, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	FA9_PIG	63-74	1	L:62-73
2	EGF_1	PS00022	EGF-like domain signature 1.	FA9_PIG	72-83	1	L:71-82
3	EGF_2	PS01186	EGF-like domain signature 2.	FA9_PIG	72-83 110-125	2	L:71-82 L:109-124
4	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	FA9_PIG	183-409	1	C:16-237
5	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	FA9_PIG	219-224	1	C:53-58
6	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	FA9_PIG	361-372	1	C:189-200

Biological Unit 1 (6, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	FA9_PIG	63-74	1	L:62-73
2	EGF_1	PS00022	EGF-like domain signature 1.	FA9_PIG	72-83	1	L:71-82
3	EGF_2	PS01186	EGF-like domain signature 2.	FA9_PIG	72-83 110-125	2	L:71-82 L:109-124
4	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	FA9_PIG	183-409	1	C:16-237
5	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	FA9_PIG	219-224	1	C:53-58
6	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	FA9_PIG	361-372	1	C:189-200

Biological Unit 2 (6, 14)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	FA9_PIG	63-74	2	L:62-73
2	EGF_1	PS00022	EGF-like domain signature 1.	FA9_PIG	72-83	2	L:71-82
3	EGF_2	PS01186	EGF-like domain signature 2.	FA9_PIG	72-83 110-125	4	L:71-82 L:109-124
4	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	FA9_PIG	183-409	2	C:16-237
5	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	FA9_PIG	219-224	2	C:53-58
6	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	FA9_PIG	361-372	2	C:189-200

Exons (0, 0)

Sequences/Alignments

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 C from PDB  Type:PROTEIN  Length:235
 aligned with FA9_PIG | P16293 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:235
                                                                                                                                                                                                                                                            409        
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402      |  -     
             FA9_PIG    183 IVGGENAKPGQFPWQVLLNGKIDAFCGGSIINEKWVVTAAHCIEPGVKITVVAGEYNTEETEPTEQRRNVIRAIPHHSYNATVNKYSHDIALLELDEPLTLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFNRGRSATILQYLKVPLVDRATCLRSTKVTIYSNMFCAGFHEGGKDSCLGDSGGPHVTEVEGTSFLTGIISWGEECAVKGKYGIYTKVSRYVNW--------    -
               SCOP domains d1x7ac_ C: Coagulation factor IXa, protease domain                                                                                                                                                                                          SCOP domains
               CATH domains 1x7aC01     1x7aC02 C:28-120,C:233-245 Trypsin-like serine proteases                                       1x7aC01 C:16-27,C:121-232 Trypsin-like serine proteases                                                            1x7aC02       CATH domains
               Pfam domains Trypsin-1x7aC01 C:16-237                                                                                                                                                                                                           -------- Pfam domains
         Sec.struct. author ....ee........eeeee......eeeeeee..eeee...........eee.................eeeeee...............eeeee................hhhhhhhhhh..eeeeee..............eeeeeeeehhhhhhh.........eeee................eeeee....eeeeeeeee..........eeeehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: C:16-237 UniProt: 183-409                                                                                                                                                                                        -------- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1x7a C   16 IVGGENAKPGQFPWQVLLNGKIDAFCGGSIINEKWVVTAAHCIEPGVKITVVAGEYNTEETEPTEQRRNVIRAIPHHSYNATVNKYSHDIALLELDEPLTLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFNRGRSATILQYLKVPLVDRATCLRSTKFTIYSNMFCAGFHEGGKDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAVKGKYGIYTKVSRYVNWIKEKTKLT  245
                                    25        35||      46        56    |   65        75        85        95||     103       113       123      |131       141   ||  152       162       172       182  |    190       200       210      |221|      230       240     
                                               36|                    60A                                 95A|                               129A|             145|                                  184A 188A                          217|  |                        
                                                38                                                         95B                                129B              147                                                                      219  |                        
                                                                                                                                                                                                                                           221A

Chain L from PDB  Type:PROTEIN  Length:97
 aligned with FA9_PIG | P16293 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:97
                                    60        70        80        90       100       110       120       130       140       
             FA9_PIG     51 QCEPNPCLNGGLCKDDINSYECWCQVGFEGKNCELDATCNIKNGRCKQFCKTGADSKVLCSCTTGYRLAPDQKSCKPAVPFPCGRVSVSHSPTTLTR  147
               SCOP domains d1x7al1 L:50-86 Factor IX (IXa)      d1x7al2 L:87-146 Factor IX (IXa)                             SCOP domains
               CATH domains 1x7aL01 L:50-85 Laminin             1x7aL02 L:86-127 Laminin                  ------------------- CATH domains
               Pfam domains -EGF-1x7aL01 L:51-81            ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....eeee....ee.....ee....hhhhh....................eee......eee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------ASX_HYDROXYL-----------------------------------EGF_2           ---------------------- PROSITE (1)
                PROSITE (2) ---------------------EGF_1       ---------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------EGF_2       ---------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                1x7a L   50 QCEPNPCLNGGLCKDDINSYECWCQVGFEGKNCELDATCNIKNGRCKQFCKTGADSKVLCSCTTGYRLAPDQKSCKPAVPFPCGRVSVSHSPTTLTR  146
                                    59        69        79        89        99       109       119       129       139

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 '\|'

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (2, 4)

Pfam Domains (2, 2)

Gene Ontology (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain C,L (FA9_PIG | P16293)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0031638	zymogen activation	The proteolytic processing of an inactive enzyme to an active form.
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.
	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.

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	1x7a
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	FA9_PIG \| P16293
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	3.4.21.22
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