1XKA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S)-(3'-AMIDINO-3-BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID

Authors :   K. Kamata, S. H. Kim

Date :   19 Mar 98 (Deposition) - 23 Mar 99 (Release) - 20 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : C,L

Keywords :   Blood Coagulation Factor, Serine Proteinase, Epidermal Growth Factor Like Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kamata, H. Kawamoto, T. Honma, T. Iwama, S. H. Kim
Structural Basis For Chemical Inhibition Of Human Blood Coagulation Factor Xa.
Proc. Natl. Acad. Sci. Usa V. 95 6630 1998
PubMed-ID: 9618463 | Reference-DOI: 10.1073/PNAS.95.12.6630
(for further references see the PDB file header)

Molecule 1 - BLOOD COAGULATION FACTOR XA
	Chains	:	L
	EC Number	:	3.4.21.6
	Fragment	:	PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	STUART FACTOR
	Tissue	:	BLOOD

Molecule 2 - BLOOD COAGULATION FACTOR XA
	Chains	:	C
	EC Number	:	3.4.21.6
	Fragment	:	PROTEOLYTIC CLEAVAGE PRODUCT, GLA DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	STUART FACTOR
	Tissue	:	BLOOD

		1	2
Asymmetric/Biological Unit	:	C	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	4PP	1	Ligand/Ion	(2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID
2	BHD	1	Mod. Amino Acid	(3S)-3-HYDROXY-L-ASPARTIC ACID
3	CA	1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP C:70 , ASN C:72 , GLN C:75 , GLU C:77 , GLU C:80	BINDING SITE FOR RESIDUE CA C 501
2	AC2	SOFTWARE	GLU C:97 , THR C:98 , TYR C:99 , PHE C:174 , ASP C:189 , ALA C:190 , GLN C:192 , SER C:195 , TRP C:215 , GLY C:216 , GLY C:218 , CYS C:220 , GLY C:226 , HOH C:517 , HOH C:519 , HOH C:578 , HOH C:583 , GLN L:56 , LYS L:79 , ASN L:80	BINDING SITE FOR RESIDUE 4PP C 500

Asymmetric/Biological Unit

No.	Residues
1	C:22	-	C:27
2	C:42	-	C:58
3	C:168	-	C:182
4	C:191	-	C:220
5	L:50	-	L:61
6	L:55	-	L:70
7	L:72	-	L:81
8	L:89	-	L:100
9	L:96	-	L:109
10	L:111	-	L:124
11	L:132	-	C:122

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

Asymmetric/Biological Unit (24, 24)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_075213	G	262	D	FA10_HUMAN	Unclassified (FA10D)	---	C	G	43	D
02	UniProt	VAR_065433	E	91	K	FA10_HUMAN	Disease (FA10D)	---	L	E	51	K
03	UniProt	VAR_065437	G	289	R	FA10_HUMAN	Disease (FA10D)	121964946	C	G	69	R
04	UniProt	VAR_065438	E	304	K	FA10_HUMAN	Disease (FA10D)	747292771	C	E	84	K
05	UniProt	VAR_065434	E	142	K	FA10_HUMAN	Unclassified (FA10D)	61753266	L	E	102	K
06	UniProt	VAR_065439	D	322	N	FA10_HUMAN	Disease (FA10D)	121964942	C	D	102	N
07	UniProt	VAR_065440	R	327	W	FA10_HUMAN	Disease (FA10D)	770119164	C	R	107	W
08	UniProt	VAR_065435	C	149	Y	FA10_HUMAN	Disease (FA10D)	---	L	C	109	Y
09	UniProt	VAR_065436	C	151	Y	FA10_HUMAN	Disease (FA10D)	---	L	C	111	Y
10	UniProt	VAR_020176	A	152	T	FA10_HUMAN	Polymorphism	3211772	L	A	112	T
11	UniProt	VAR_065441	V	338	M	FA10_HUMAN	Disease (FA10D)	121964947	C	V	118	M
12	UniProt	VAR_065442	E	350	K	FA10_HUMAN	Disease (FA10D)	372309538	C	E	129	K
13	UniProt	VAR_065443	T	358	M	FA10_HUMAN	Disease (FA10D)	768222784	C	T	135	M
14	UniProt	VAR_065444	G	363	S	FA10_HUMAN	Disease (FA10D)	---	C	G	140	S
15	UniProt	VAR_065445	R	366	C	FA10_HUMAN	Disease (FA10D)	104894392	C	R	143	C
16	UniProt	VAR_065446	S	374	P	FA10_HUMAN	Disease (FA10D)	121964941	C	S	152	P
17	UniProt	VAR_072751	V	382	A	FA10_HUMAN	Disease (FA10D)	---	C	V	160	A
18	UniProt	VAR_065447	P	383	S	FA10_HUMAN	Disease (FA10D)	121964940	C	P	161	S
19	UniProt	VAR_065448	C	390	F	FA10_HUMAN	Disease (FA10D)	199778916	C	C	168	F
20	UniProt	VAR_065449	C	404	R	FA10_HUMAN	Disease (FA10D)	---	C	C	182	R
21	UniProt	VAR_065450	G	406	S	FA10_HUMAN	Disease (FA10D)	376163818	C	G	184	S
22	UniProt	VAR_065451	G	420	R	FA10_HUMAN	Disease (FA10D)	750759634	C	G	196	R
23	UniProt	VAR_072752	G	421	D	FA10_HUMAN	Disease (FA10D)	758726161	C	G	197	D
24	UniProt	VAR_065452	K	448	N	FA10_HUMAN	Disease (FA10D)	---	C	K	224	N

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

Asymmetric/Biological Unit (6, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASX_HYDROXYL	PS00010	Aspartic acid and asparagine hydroxylation site.	FA10_HUMAN	101-112	1	L:61-72
2	EGF_1	PS00022	EGF-like domain signature 1.	FA10_HUMAN	110-121	1	L:70-81
3	EGF_2	PS01186	EGF-like domain signature 2.	FA10_HUMAN	110-121 149-164	2	L:70-81 L:109-124
4	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	FA10_HUMAN	235-467	1	C:16-243
5	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	FA10_HUMAN	272-277	1	C:53-58
6	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	FA10_HUMAN	413-424	1	C:189-200

Asymmetric/Biological Unit (5, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000375559	1b	ENSE00001885902	chr13:113777132-113777239	108	FA10_HUMAN	1-24	24	0	-	-
1.2	ENST00000375559	2	ENSE00001757906	chr13:113783766-113783926	161	FA10_HUMAN	24-77	54	0	-	-
1.4	ENST00000375559	4	ENSE00001666002	chr13:113792771-113792795	25	FA10_HUMAN	78-86	9	0	-	-
1.5	ENST00000375559	5	ENSE00001614193	chr13:113793671-113793784	114	FA10_HUMAN	86-124	39	1	- L:49-84	- 36
1.6c	ENST00000375559	6c	ENSE00000862532	chr13:113795233-113795364	132	FA10_HUMAN	124-168	45	1	- L:84-128	- 45
1.7a	ENST00000375559	7a	ENSE00001710199	chr13:113798165-113798409	245	FA10_HUMAN	168-249	82	2	C:16-30 L:128-139	15 12
1.8e	ENST00000375559	8e	ENSE00000862534	chr13:113801693-113801810	118	FA10_HUMAN	250-289	40	1	C:31-69 -	40 -
1.9c	ENST00000375559	9c	ENSE00001616173	chr13:113803230-113803843	614	FA10_HUMAN	289-488	200	1	C:69-245 (gaps) -	183 -

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 C from PDB  Type:PROTEIN  Length:235
 aligned with FA10_HUMAN | P00742 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:235
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     
          FA10_HUMAN    235 IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTR  469
               SCOP domains d1xkac_ C: Coagulation factor Xa, protease domain                                                                                                                                                                                           SCOP domains
               CATH domains 1xkaC01     1xkaC02 C:28-120,C:233-245 Trypsin-like serine proteases                                      1xkaC01 C:16-27,C:121-232 Trypsin-like serine proteases                                                             1xkaC02       CATH domains
               Pfam domains Trypsin-1xkaC01 C:16-238                                                                                                                                                                                                            ------- Pfam domains
         Sec.struct. author ..............eeeeee....eeeeee.....eeee.hhhhh....eeeee............eee.eeeeee.............eeeee.................hhhhhhh.....eeeeee..............eeeeee...hhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeeehhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------D--------------------------R--------------K-----------------N----W----------M-----------K-------M----S--C-------P-------AS------F-------------R-S-------------RD--------------------------N--------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: C:16-243 UniProt: 235-467                                                                                                                                                                                              -- PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.7a      Exon 1.8e  PDB: C:31-69 UniProt: 250-289------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.9c  PDB: C:69-245 (gaps) UniProt: 289-488 [INCOMPLETE]                                                                                                                         Transcript 1 (2)
                1xka C   16 IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTR  245
                                    25        35        45        55      | 64        74        84        94       104       114       124|     131B       141     ||152       162       172       182   ||  190       200       210       221  |    230       240     
                                                                        61A                                                            124A    131A|             147|                                 185A|                              218|   |                      
                                                                                                                                                131B              149                                  185B                               220   |                      
                                                                                                                                                                                                                                             223A

Chain L from PDB  Type:PROTEIN  Length:91
 aligned with FA10_HUMAN | P00742 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:91
                                    98       108       118       128       138       148       158       168       178 
          FA10_HUMAN     89 QCETSPCQNQGKCKDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLER  179
               SCOP domains d1xkal1 L:49-86                       d1xkal2 L:87-139 Factor X, N-terminal module          SCOP domains
               CATH domains 1xkaL01 L:49-85 Laminin              1xkaL02 L:86-135 Laminin                          ---- CATH domains
               Pfam domains -EGF-1xkaL01 L:50-80            ----------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee......eee....................hhhh...eeee....eeee....eee......eee............. Sec.struct. author
                 SAPs(SNPs) --K--------------------------------------------------K------Y-YT--------------------------- SAPs(SNPs)
                PROSITE (1) ------------ASX_HYDROXYL------------------------------------EGF_2           --------------- PROSITE (1)
                PROSITE (2) ---------------------EGF_2       ---------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------EGF_1       ---------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.5  PDB: L:49-84 [INCOMPLETE] -------------------------------------------Exon 1.7a    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.6c  PDB: L:84-128 UniProt: 124-168    ----------- Transcript 1 (2)
                1xka L   49 QCETSPCQNQGKCKdGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLER  139
                                    58    |   68        78        88        98       108       118       128       138 
                                         63-BHD

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: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Coagulation factor Xa, protease domain (48)

Human (Homo sapiens) [TaxId: 9606] (47)

d1xkac_

Class: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: EGF/Laminin (347)

Family: EGF-type module (304)

Protein domain: Factor X, N-terminal module (81)

Human (Homo sapiens) [TaxId: 9606] (76)

2a	d1xkal1	L:49-86
2b	d1xkal2	L:87-139

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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	1xkaC01	C:16-27,C:121-232
1b	1xkaC02	C:28-120,C:233-245

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

Human (Homo sapiens) (195)

2a	1xkaL02	L:86-135
2b	1xkaL01	L:49-85

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EGF (60)

Family: EGF (31)

Homo sapiens (Human) (25)

EGF-1xkaL01

L:50-80

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

Trypsin-1xkaC01

C:16-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain C,L (FA10_HUMAN | P00742)

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:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
	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: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:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	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:0007598	blood coagulation, extrinsic pathway	A protein activation cascade that contributes to blood coagulation and consists of the self-limited process linking exposure and activation of tissue factor to the activation of clotting factor X.
	GO:0007597	blood coagulation, intrinsic pathway	A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0017187	peptidyl-glutamic acid carboxylation	The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0051897	positive regulation of protein kinase B signaling	Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006465	signal peptide processing	The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
	GO:0005796	Golgi lumen	The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	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:0031233	intrinsic component of external side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	1xka
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	FA10_HUMAN \| P00742
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	3.4.21.6
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	227600
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(no "Related Entries Specified in the PDB File" available for 1XKA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (11, 11)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (24, 24)

PROSITE Motifs (6, 6)

Exons (5, 6)

Sequences/Alignments

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SCOP Domains (2, 3)

CATH Domains (2, 4)

Pfam Domains (2, 2)

Gene Ontology (22, 22)

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