1J35 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CA(II)-BOUND GLA DOMAIN OF FACTOR IX COMPLEXED WITH BINDING PROTEIN

Authors :   Y. Shikamoto, T. Morita, Z. Fujimoto, H. Mizuno

Date :   20 Jan 03 (Deposition) - 08 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Magnesium Ion, Calcium Ion, Gla Domain, Protein Binding/Blood Clotting Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Shikamoto, T. Morita, Z. Fujimoto, H. Mizuno
Crystal Structure Of Mg2+- And Ca2+-Bound Gla Domain Of Factor Ix Complexed With Binding Protein
J. Biol. Chem. V. 278 24090 2003
PubMed-ID: 12695512 | Reference-DOI: 10.1074/JBC.M300650200
(for further references see the PDB file header)

Molecule 1 - COAGULATION FACTOR IX-BINDING PROTEIN A CHAIN
	Chains	:	A
	Organism Scientific	:	TRIMERESURUS FLAVOVIRIDIS
	Organism Taxid	:	88087
	Secretion	:	VENOM
	Synonym	:	COAGULATION FACTOR IX BINDING PROTEIN CHAIN A

Molecule 2 - COAGULATION FACTOR IX-BINDING PROTEIN B CHAIN
	Chains	:	B
	Organism Scientific	:	TRIMERESURUS FLAVOVIRIDIS
	Organism Taxid	:	88087
	Secretion	:	VENOM

Molecule 3 - COAGULATION FACTOR IX
	Chains	:	C
	EC Number	:	3.4.21.22
	Fragment	:	GLA DOMAIN
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Secretion	:	PLASMA

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 22)

No.	Name	Count	Type	Full Name
1	CA	10	Ligand/Ion	CALCIUM ION
2	CGU	12	Mod. Amino Acid	GAMMA-CARBOXY-GLUTAMIC ACID

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:98 , HOH B:617 , CGU C:426 , CGU C:430	BINDING SITE FOR RESIDUE CA C 501
02	AC2	SOFTWARE	HOH B:643 , CGU C:408 , CGU C:427 , CGU C:430 , HOH C:655	BINDING SITE FOR RESIDUE CA C 502
03	AC3	SOFTWARE	CGU C:408 , CGU C:417 , CGU C:427 , CGU C:430 , HOH C:625 , HOH C:636 , HOH C:661	BINDING SITE FOR RESIDUE CA C 503
04	AC4	SOFTWARE	TYR C:401 , ASN C:402 , CGU C:407 , CGU C:408 , CGU C:417 , CGU C:427	BINDING SITE FOR RESIDUE CA C 504
05	AC5	SOFTWARE	TYR C:401 , CGU C:407 , CGU C:417 , CGU C:421 , HOH C:692 , HOH C:705	BINDING SITE FOR RESIDUE CA C 505
06	AC6	SOFTWARE	CGU C:421 , HOH C:675 , HOH C:708 , HOH C:740 , HOH C:810	BINDING SITE FOR RESIDUE CA C 506
07	AC7	SOFTWARE	CGU C:415 , CGU C:420 , HOH C:776	BINDING SITE FOR RESIDUE CA C 507
08	AC8	SOFTWARE	CGU C:436 , CGU C:440 , HOH C:654 , HOH C:725 , HOH C:840	BINDING SITE FOR RESIDUE CA C 508
09	AC9	SOFTWARE	SER A:41 , GLU A:43 , GLU A:47 , GLU A:128 , HOH A:603 , HOH A:823	BINDING SITE FOR RESIDUE CA A 511
10	BC1	SOFTWARE	SER B:241 , GLN B:243 , GLU B:247 , GLU B:320 , HOH B:822 , HOH B:829	BINDING SITE FOR RESIDUE CA B 512

Asymmetric/Biological Unit

No.	Residues
1	A:2	-	A:13
2	A:30	-	A:127
3	A:79	-	B:275
4	A:102	-	A:119
5	B:202	-	B:213
6	B:230	-	B:319
7	B:296	-	B:311
8	C:418	-	C:423

(no "Cis Peptide Bond" information available for 1J35)

(no "SAP(SNP)/Variant" information available for 1J35)

Asymmetric/Biological Unit (4, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	SLA_PROFL	9-128	1	A:9-128
				SL9A_PROFL	32-151	1	A:9-128
				SL9B_PROFL	32-143	1	B:209-320
2	GLA_2	PS50998	Gla domain profile.	FA9_BOVIN	47-93	1	C:401-446
3	GLA_1	PS00011	Vitamin K-dependent carboxylation domain.	FA9_BOVIN	63-88	1	C:417-442
4	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	SLA_PROFL	102-127	1	A:102-127
				SL9B_PROFL	119-142	1	B:296-319
				SL9A_PROFL	125-150	1	A:102-127

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000005227	1	ENSBTAE00000424634	X:12957216-12957316	101	FA9_BOVIN	1-30	30	0	-	-
1.2	ENSBTAT00000005227	2	ENSBTAE00000425150	X:12975755-12975918	164	FA9_BOVIN	30-84	55	1	C:401-438	38
1.3	ENSBTAT00000005227	3	ENSBTAE00000410831	X:12976116-12976140	25	FA9_BOVIN	85-93	9	1	C:439-446	8
1.4	ENSBTAT00000005227	4	ENSBTAE00000387324	X:12980325-12980438	114	FA9_BOVIN	93-131	39	0	-	-
1.5	ENSBTAT00000005227	5	ENSBTAE00000388223	X:12987557-12987685	129	FA9_BOVIN	131-174	44	0	-	-
1.6b	ENSBTAT00000005227	6b	ENSBTAE00000041994	X:12990058-12990263	206	FA9_BOVIN	174-242	69	0	-	-
1.7	ENSBTAT00000005227	7	ENSBTAE00000041996	X:12999018-12999132	115	FA9_BOVIN	243-281	39	0	-	-
1.8	ENSBTAT00000005227	8	ENSBTAE00000041998	X:13001262-13003332	2071	FA9_BOVIN	281-462	182	0	-	-

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:129
 aligned with SL9A_PROFL | P23806 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:129
                                    33        43        53        63        73        83        93       103       113       123       133       143         
           SL9A_PROFL    24 DCLSGWSSYEGHCYKAFEKYKTWEDAERVCTEQAKGAHLVSIESSGEADFVAQLVTQNMKRLDFYIWIGLRVQGKVKQCNSEWSDGSSVSYENWIEAESKTCLGLEKETDFRKWVNIYCGQQNPFVCEA 152
               SCOP domains d1j35a_ A: Snake coagglutinin alpha chain                                                                                         SCOP domains
               CATH domains 1j35A00 A:1-129 Mannose-Binding Protein A, subunit A                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhh........eeeeeee......................hhhhh..eeeehhhhh....eee.....eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------C_TYPE_LECTIN_2  PDB: A:9-128 UniProt: 32-151                                                                           - PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) -----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           -- PROSITE (6)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j35 A   1 DCPSGWSSYEGHCYKPFKLYKTWDDAERFCTEQAKGGHLVSIESAGEADFVAQLVTENIQNTKSYVWIGLRVQGKEKQCSSEWSDGSSVSYENWIEAESKTCLGLEKETGFRKWVNIYCGQQNPFVCEA 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain A from PDB  Type:PROTEIN  Length:129
 aligned with SLA_PROFL | Q7LZ71 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
            SLA_PROFL     1 DCPSGWSSYEGHCYKPFKLYKTWDDAERFCTEQAKGGHLVSIESAGEADFVAQLVTENIQNTKSYVWIGLRVQGKEKQCSSEWSDGSSVSYENWIEAESKTCLGLEKETGFRKWVNIYCGQQNPFVCEA 129
               SCOP domains d1j35a_ A: Snake coagglutinin alpha chain                                                                                         SCOP domains
               CATH domains 1j35A00 A:1-129 Mannose-Binding Protein A, subunit A                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhh........eeeeeee......................hhhhh..eeeehhhhh....eee.....eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:9-128 UniProt: 9-128                                                                            - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           -- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j35 A   1 DCPSGWSSYEGHCYKPFKLYKTWDDAERFCTEQAKGGHLVSIESAGEADFVAQLVTENIQNTKSYVWIGLRVQGKEKQCSSEWSDGSSVSYENWIEAESKTCLGLEKETGFRKWVNIYCGQQNPFVCEA 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with SL9B_PROFL | P23807 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:123
                                    33        43        53        63        73        83        93       103       113       123       133       143   
           SL9B_PROFL    24 DCPSDWSSYEGHCYKPFSEPKNWADAENFCTQQHAGGHLVSFQSSEEADFVVKLAFQTFGHSIFWMGLSNVWNQCNWQWSNAAMLRYKAWAEESYCVYFKSTNNKWRSRACRMMAQFVCEFQA 146
               SCOP domains d1j35b_ B: Snake coagglutinin beta chain                                                                                    SCOP domains
               CATH domains 1j35B00 B:201-323 Mannose-Binding Protein A, subunit A                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhh......ee....hhhhhhhhhhhhhhhhh..eee...........eee...............eeeeee......eeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------C_TYPE_LECTIN_2  PDB: B:209-320 UniProt: 32-143                                                                 --- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -----------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (5)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j35 B 201 DCPSDWSSYEGHCYKPFSEPKNWADAENFCTQQHAGGHLVSFQSSEEADFVVKLAFQTFGHSIFWMGLSNVWNQCNWQWSNAAMLRYKAWAEESYCVYFKSTNNKWRSRACRMMAQFVCEFQA 323
                                   210       220       230       240       250       260       270       280       290       300       310       320

Chain C from PDB  Type:PROTEIN  Length:46
 aligned with FA9_BOVIN | P00741 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:46
                                    56        66        76        86      
            FA9_BOVIN    47 YNSGKLEEFVRGNLERECKEEKCSFEEAREVFENTEKTTEFWKQYV  92
               SCOP domains d1j35c_ C: Coagulation factor IX (IXa)         SCOP domains
               CATH domains 1j35C00 C:401-446 Coagulation Factor IX        CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------- PROSITE (3)
                PROSITE (4) GLA_2  PDB: C:401-446 UniProt: 47-93           PROSITE (4)
                PROSITE (5) ----------------GLA_1  PDB: C:417-442     ---- PROSITE (5)
               Transcript 1 Exon 1.2  PDB: C:401-438 [INCOMPLETE] Exon 1.3 Transcript 1
                 1j35 C 401 YNSGKLeeFVRGNLeReCKeeKCSFeeAReVFeNTeKTTeFWKQYV 446
                                  |410    | |420|    ||430  |  | 440      
                                  ||      | |  ||    ||  |  |  |   |      
                                407-CGU   | |  ||    ||  |  |  |   |      
                                 408-CGU  | |  ||    ||  |  |  |   |      
                                        415-CGU||    ||  |  |  |   |      
                                          417-CGU    ||  |  |  |   |      
                                             420-CGU ||  |  |  |   |      
                                              421-CGU||  |  |  |   |      
                                                   426-CGU  |  |   |      
                                                    427-CGU |  |   |

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Mannose-Binding Protein A; Chain A (180)

Homologous Superfamily: Mannose-Binding Protein A, subunit A (180)

Trimeresurus flavoviridis. Organism_taxid: 88087. (7)

1a	1j35A00	A:1-129
1b	1j35B00	B:201-323

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Coagulation Factor IX (11)

Homologous Superfamily: Coagulation Factor IX (11)

Trimeresurus flavoviridis. Organism_taxid: 88087. (2)

1j35C00

C:401-446

(no "Pfam Domain" information available for 1J35)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SL9A_PROFL | P23806)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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 A (SLA_PROFL | Q7LZ71)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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 B (SL9B_PROFL | P23807)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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 C (FA9_BOVIN | P00741)

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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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: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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1j35)

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	1j35
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	3.4.21.22
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UniProtKB/Swiss-Prot
	FA9_BOVIN \| P00741	:	1j34
	SL9A_PROFL \| P23806	:	1ixx 1j34
	SL9B_PROFL \| P23807	:	1bj3 1ixx 1j34 1x2t 1x2w
	SLA_PROFL \| Q7LZ71	:	1bj3 1j34 1x2t 1x2w

1bj3	A PART OF THIS COMPLEX
1iod	MOLECULAR REPLACEMENT MODEL
1j34	THE SAME COMPLEX WITH MG(II) AND CA(II) IONS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 22)

Sites (10, 10)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 6)

Exons (2, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (15, 23)

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