3JTC - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   IMPORTANCE OF MG2+ IN THE CA2+-DEPENDENT FOLDING OF THE GAMMA-CARBOXYGLUTAMIC ACID DOMAINS OF VITAMIN K-DEPENDENT CLOTTING AND ANTICLOTTING PROTEINS

Authors :   S. P. Bajaj, K. Vadivel, S. Agah, D. Cascio, S. Krishnaswamy, C. Esmon, K. Padmanabhan

Date :   11 Sep 09 (Deposition) - 06 Apr 11 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Gla (Gamma-Carboxyglutamic Acid) Residues, Phospholipid Binding Groove, Ca Ion Binding, Blood Clotting, Blood Coagulation, Disulfide Bond, Glycoprotein, Membrane, Receptor, Transmembrane, Cleavage On Pair Of Basic Residues, Disease Mutation, Egf-Like Domain, Gamma- Carboxyglutamic Acid, Hydrolase, Hydroxylation, Protease, Serine Protease, Thrombophilia, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Vadivel, S. Agah, A. S. Messer, D. Cascio, M. S. Bajaj, S. Krishnaswamy, C. T. Esmon, K. Padmanabhan, S. P. Bajaj
Structural And Functional Studies Of Gamma-Carboxyglutamic Acid Domains Of Factor Viia And Activated Protein C: Role O Magnesium At Physiological Calcium.
J. Mol. Biol. V. 425 1961 2013
PubMed-ID: 23454357 | Reference-DOI: 10.1016/J.JMB.2013.02.017

Molecule 1 - ENDOTHELIAL PROTEIN C RECEPTOR
	Chains	:	A, B
	Fragment	:	EXTRACELLULAR DOMAIN (UNP RESIDUES 18-210)
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ENDOTHELIAL CELL PROTEIN C RECEPTOR, ACTIVATED PROTEIN C RECEPTOR, APC RECEPTOR

Molecule 2 - VITAMIN K-DEPENDENT PROTEIN C
	Chains	:	C, D
	EC Number	:	3.4.21.69
	Fragment	:	GLA DOMAIN (UNP RESIDUES 43-75)
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CLEAVAGE HAPPENED DURING CRYSTALLIZATION AND THE CRYSTAL CONTAINS ONLY THE N-TERMINAL DOMAIN (GLA DOMAIN) OF PROTEIN C.
	Synonym	:	AUTOPROTHROMBIN IIA, ANTICOAGULANT PROTEIN C, BLOOD COAGULATION FACTOR XIV, VITAMIN K-DEPENDENT PROTEIN C LIGHT CHAIN, VITAMIN K-DEPENDENT PROTEIN C HEAVY CHAIN, ACTIVATION PEPTIDE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 40)

No.	Name	Count	Type	Full Name
1	CA	10	Ligand/Ion	CALCIUM ION
2	CGU	18	Mod. Amino Acid	GAMMA-CARBOXY-GLUTAMIC ACID
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	PTY	2	Ligand/Ion	PHOSPHATIDYLETHANOLAMINE

Biological Unit 1 (4, 13)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CGU	9	Mod. Amino Acid	GAMMA-CARBOXY-GLUTAMIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	PTY	1	Ligand/Ion	PHOSPHATIDYLETHANOLAMINE

Biological Unit 2 (3, 13)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CGU	9	Mod. Amino Acid	GAMMA-CARBOXY-GLUTAMIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6	PTY	1	Ligand/Ion	PHOSPHATIDYLETHANOLAMINE

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:14 , ILE A:16 , GLN A:28 , ASN A:30 , HOH A:785	BINDING SITE FOR RESIDUE NAG A 603
02	AC2	SOFTWARE	ALA A:90 , PRO A:92 , ASN A:119 , HOH A:729	BINDING SITE FOR RESIDUE NAG A 604
03	AC3	SOFTWARE	ASN A:155	BINDING SITE FOR RESIDUE NDG A 605
04	AC4	SOFTWARE	LEU A:14 , ASN A:30 , HIS A:39 , LEU A:69 , TYR A:72 , GLN A:75 , PHE A:76 , ARG A:156 , THR A:157 , GLU A:160 , GLU A:163 , PHE A:164 , CYS A:169 , HOH A:700 , HOH A:701 , HOH A:702	BINDING SITE FOR RESIDUE PTY A 606
05	AC5	SOFTWARE	HIS B:12 , GLN B:28 , ASN B:30 , ALA B:31 , SER B:32 , HOH B:637 , HOH B:653 , HOH B:667 , HOH B:722	BINDING SITE FOR RESIDUE NAG B 600
06	AC6	SOFTWARE	ALA B:90 , PRO B:92 , ASN B:119 , HOH B:626 , HOH B:701	BINDING SITE FOR RESIDUE NAG B 601
07	AC7	SOFTWARE	ASN B:155 , HOH B:660 , HOH B:686	BINDING SITE FOR RESIDUE NAG B 602
08	AC8	SOFTWARE	LEU B:11 , ASN B:30 , HIS B:39 , LEU B:69 , TYR B:72 , ARG B:156 , THR B:157 , GLU B:160 , GLU B:163 , PHE B:164 , CYS B:169 , HOH B:638 , HOH B:642 , HOH B:679 , HOH B:714	BINDING SITE FOR RESIDUE PTY B 607
09	AC9	SOFTWARE	GLU A:86 , HOH A:615 , CGU C:25 , CGU C:29	BINDING SITE FOR RESIDUE MG C 34
10	BC1	SOFTWARE	GLU A:86 , CGU C:7 , CGU C:26 , CGU C:29 , HOH C:47	BINDING SITE FOR RESIDUE CA C 35
11	BC2	SOFTWARE	CGU C:7 , CGU C:16 , CGU C:26 , CGU C:29 , HOH C:56 , HOH C:57 , HOH C:74	BINDING SITE FOR RESIDUE CA C 36
12	BC3	SOFTWARE	ALA C:1 , ASN C:2 , CGU C:6 , CGU C:7 , CGU C:16 , CGU C:26	BINDING SITE FOR RESIDUE CA C 37
13	BC4	SOFTWARE	ALA C:1 , CGU C:6 , CGU C:16 , CGU C:20 , HOH C:59	BINDING SITE FOR RESIDUE CA C 38
14	BC5	SOFTWARE	CGU C:20 , HOH C:63 , HOH C:66 , HOH C:79 , HOH C:80	BINDING SITE FOR RESIDUE CA C 39
15	BC6	SOFTWARE	CGU C:14 , CGU C:19 , HOH C:67 , HOH C:99	BINDING SITE FOR RESIDUE MG C 40
16	BC7	SOFTWARE	GLU B:86 , HOH B:658 , CGU D:25 , CGU D:29	BINDING SITE FOR RESIDUE MG D 34
17	BC8	SOFTWARE	GLU B:86 , CGU D:7 , CGU D:26 , CGU D:29 , HOH D:54	BINDING SITE FOR RESIDUE CA D 35
18	BC9	SOFTWARE	CGU D:7 , CGU D:16 , CGU D:26 , CGU D:29 , HOH D:56 , HOH D:57 , HOH D:60	BINDING SITE FOR RESIDUE CA D 36
19	CC1	SOFTWARE	ALA D:1 , ASN D:2 , CGU D:6 , CGU D:7 , CGU D:16 , CGU D:26	BINDING SITE FOR RESIDUE CA D 37
20	CC2	SOFTWARE	ALA D:1 , CGU D:6 , CGU D:16 , CGU D:20 , HOH D:77	BINDING SITE FOR RESIDUE CA D 38
21	CC3	SOFTWARE	CGU D:20 , HOH D:58 , HOH D:69 , HOH D:70 , HOH D:75	BINDING SITE FOR RESIDUE CA D 39
22	CC4	SOFTWARE	CGU D:14 , CGU D:19 , HOH D:68 , HOH D:87	BINDING SITE FOR RESIDUE MG D 40

Asymmetric Unit

No.	Residues
1	A:101	-	A:169
2	B:101	-	B:169
3	C:17	-	C:22
4	D:17	-	D:22

Asymmetric Unit

No.	Residues
1	Phe A:91	-	Pro A:92
2	Phe B:91	-	Pro B:92

Asymmetric Unit (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006639	A	43	T	PROC_HUMAN	Polymorphism	767626189	C/D	A	1	T
2	UniProt	VAR_006640	E	49	D	PROC_HUMAN	Unclassified	---	C/D	E	7	D
3	UniProt	VAR_006641	R	51	C	PROC_HUMAN	Polymorphism	764546127	C/D	R	9	C
4	UniProt	VAR_006643	R	57	G	PROC_HUMAN	Unclassified	---	C/D	R	15	G
5	UniProt	VAR_006644	R	57	Q	PROC_HUMAN	Polymorphism	574949343	C/D	R	15	Q
6	UniProt	VAR_006642	R	57	W	PROC_HUMAN	Disease (THPH3)	757583846	C/D	R	15	W
7	UniProt	VAR_006645	E	62	A	PROC_HUMAN	Disease (THPH3)	121918148	C/D	E	20	A
8	UniProt	VAR_074296	K	70	E	PROC_HUMAN	Polymorphism	199469481	C/D	K	28	E

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

Biological Unit 1 (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006639	A	43	T	PROC_HUMAN	Polymorphism	767626189	C	A	1	T
2	UniProt	VAR_006640	E	49	D	PROC_HUMAN	Unclassified	---	C	E	7	D
3	UniProt	VAR_006641	R	51	C	PROC_HUMAN	Polymorphism	764546127	C	R	9	C
4	UniProt	VAR_006643	R	57	G	PROC_HUMAN	Unclassified	---	C	R	15	G
5	UniProt	VAR_006644	R	57	Q	PROC_HUMAN	Polymorphism	574949343	C	R	15	Q
6	UniProt	VAR_006642	R	57	W	PROC_HUMAN	Disease (THPH3)	757583846	C	R	15	W
7	UniProt	VAR_006645	E	62	A	PROC_HUMAN	Disease (THPH3)	121918148	C	E	20	A
8	UniProt	VAR_074296	K	70	E	PROC_HUMAN	Polymorphism	199469481	C	K	28	E

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

Biological Unit 2 (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006639	A	43	T	PROC_HUMAN	Polymorphism	767626189	D	A	1	T
2	UniProt	VAR_006640	E	49	D	PROC_HUMAN	Unclassified	---	D	E	7	D
3	UniProt	VAR_006641	R	51	C	PROC_HUMAN	Polymorphism	764546127	D	R	9	C
4	UniProt	VAR_006643	R	57	G	PROC_HUMAN	Unclassified	---	D	R	15	G
5	UniProt	VAR_006644	R	57	Q	PROC_HUMAN	Polymorphism	574949343	D	R	15	Q
6	UniProt	VAR_006642	R	57	W	PROC_HUMAN	Disease (THPH3)	757583846	D	R	15	W
7	UniProt	VAR_006645	E	62	A	PROC_HUMAN	Disease (THPH3)	121918148	D	E	20	A
8	UniProt	VAR_074296	K	70	E	PROC_HUMAN	Polymorphism	199469481	D	K	28	E

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLA_1	PS00011	Vitamin K-dependent carboxylation domain.	PROC_HUMAN	58-83	2	C:16-33 D:16-33

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLA_1	PS00011	Vitamin K-dependent carboxylation domain.	PROC_HUMAN	58-83	1	C:16-33 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLA_1	PS00011	Vitamin K-dependent carboxylation domain.	PROC_HUMAN	58-83	1	- D:16-33

Asymmetric Unit (4, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000216968	3a	ENSE00001463636	chr20:33759774-33760027	254	EPCR_HUMAN	1-24	24	1	A:7-7 -	1 -
1.4	ENST00000216968	4	ENSE00000661565	chr20:33762505-33762756	252	EPCR_HUMAN	24-108	85	2	A:7-91 B:8-91	85 84
1.5	ENST00000216968	5	ENSE00000661566	chr20:33763971-33764249	279	EPCR_HUMAN	108-201	94	2	A:91-178 B:91-180	88 90
1.6a	ENST00000216968	6a	ENSE00001463602	chr20:33764501-33765164	664	EPCR_HUMAN	201-238	38	0	-	-

2.1a	ENST00000234071	1a	ENSE00001747079	chr2:128176003-128176068	66	PROC_HUMAN	-	0	0	-	-
2.2e	ENST00000234071	2e	ENSE00000857263	chr2:128177498-128177588	91	PROC_HUMAN	1-24	24	0	-	-
2.3a	ENST00000234071	3a	ENSE00001019166	chr2:128178859-128179025	167	PROC_HUMAN	24-79	56	2	C:1-33 D:1-33	33 33
2.4a	ENST00000234071	4a	ENSE00001657237	chr2:128180493-128180517	25	PROC_HUMAN	80-88	9	0	-	-
2.4h	ENST00000234071	4h	ENSE00000775732	chr2:128180610-128180747	138	PROC_HUMAN	88-134	47	0	-	-
2.4k	ENST00000234071	4k	ENSE00001019181	chr2:128180850-128180984	135	PROC_HUMAN	134-179	46	0	-	-
2.5b	ENST00000234071	5b	ENSE00000775730	chr2:128183661-128183803	143	PROC_HUMAN	179-226	48	0	-	-
2.6	ENST00000234071	6	ENSE00000775729	chr2:128184681-128184798	118	PROC_HUMAN	227-266	40	0	-	-
2.7d	ENST00000234071	7d	ENSE00001853552	chr2:128185933-128186822	890	PROC_HUMAN	266-461	196	0	-	-

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 A from PDB  Type:PROTEIN  Length:172
 aligned with EPCR_HUMAN | Q9UNN8 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:172
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193  
           EPCR_HUMAN    24 GLQRLHMLQISYFRDPYHVWYQGNASLGGHLTHVLEGPDTNTTIIQLQPLQEPESWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNGSSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHIS 195
               SCOP domains d3jtca_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee..eeeeeeeeee..eeeeeeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.......eeeeeeee..eeeeeee....eeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------------------------Exon 1.5  PDB: A:91-178 UniProt: 108-201 [INCOMPLETE]                                    Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: A:7-91 UniProt: 24-108                                                --------------------------------------------------------------------------------------- Transcript 1 (2)
                 3jtc A   7 GLQRLHMLQISYFRDPYHVWYQGNASLGGHLTHVLEGPDTNTTIIQLQPLQEPESWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNGSSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHIS 178
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with EPCR_HUMAN | Q9UNN8 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:173
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   
           EPCR_HUMAN    25 LQRLHMLQISYFRDPYHVWYQGNASLGGHLTHVLEGPDTNTTIIQLQPLQEPESWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNGSSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHISAE 197
               SCOP domains d3jtcb_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------MHC_I-3jtcB01 B:53-180                                                                                                           Pfam domains (1)
           Pfam domains (2) ---------------------------------------------MHC_I-3jtcB02 B:53-180                                                                                                           Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeeee..eeeeeeeeee..eeeeeeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee........eeeeeeee..eeeeeee....eeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -----------------------------------------------------------------------------------Exon 1.5  PDB: B:91-180 UniProt: 108-201 [INCOMPLETE]                                      Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: B:8-91 UniProt: 24-108 [INCOMPLETE]                                  ----------------------------------------------------------------------------------------- Transcript 1 (2)
                 3jtc B   8 LQRLHMLQISYFRDPYHVWYQGNASLGGHLTHVLEGPDTNTTIIQLQPLQEPESWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNGSSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHISAE 180
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177

Chain C from PDB  Type:PROTEIN  Length:33
 aligned with PROC_HUMAN | P04070 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:33
                                    52        62        72   
           PROC_HUMAN    43 ANSFLEELRHSSLERECIEEICDFEEAKEIFQN  75
               SCOP domains d3jtcc_ C:                        SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..hhhhhhh....hhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) T-----D-C-----G----A-------E----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------Q------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------W------------------ SAPs(SNPs) (3)
                    PROSITE ---------------GLA_1  PDB: C:16-3 PROSITE
               Transcript 2 Exon 2.3a  PDB: C:1-33            Transcript 2
                 3jtc C   1 ANSFLeeLRHSSLeReCIeeICDFeeAKeIFQN  33
                                 || 10   | |  20    ||  30   
                                 6-CGU  14-CGU||    ||  |    
                                  7-CGU   16-CGU    ||  |    
                                             19-CGU ||  |    
                                              20-CGU||  |    
                                                   25-CGU    
                                                    26-CGU   
                                                       29-CGU

Chain D from PDB  Type:PROTEIN  Length:33
 aligned with PROC_HUMAN | P04070 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:33
                                    52        62        72   
           PROC_HUMAN    43 ANSFLEELRHSSLERECIEEICDFEEAKEIFQN  75
               SCOP domains d3jtcd_ D:                        SCOP domains
               CATH domains --------------------------------- CATH domains
           Pfam domains (1) ----Gla-3jtcD01 D:5-33            Pfam domains (1)
           Pfam domains (2) ----Gla-3jtcD02 D:5-33            Pfam domains (2)
         Sec.struct. author ....hhhhh..hhhhhhh....hhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) T-----D-C-----G----A-------E----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------Q------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------W------------------ SAPs(SNPs) (3)
                    PROSITE ---------------GLA_1  PDB: D:16-3 PROSITE
               Transcript 2 Exon 2.3a  PDB: D:1-33            Transcript 2
                 3jtc D   1 ANSFLeeLRHSSLeReCIeeICDFeeAKeIFQN  33
                                 || 10   | |  20    ||  30   
                                 6-CGU  14-CGU||    ||  |    
                                  7-CGU   16-CGU    ||  |    
                                             19-CGU ||  |    
                                              20-CGU||  |    
                                                   25-CGU    
                                                    26-CGU   
                                                       29-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 '\|'

(no "CATH Domain" information available for 3JTC)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MHC (252)

Family: MHC_I (210)

Homo sapiens (Human) (144)

1a	MHC_I-3jtcB01	B:53-180
1b	MHC_I-3jtcB02	B:53-180

Clan: no clan defined [family: Gla] (24)

Family: Gla (24)

Homo sapiens (Human) (14)

2a	Gla-3jtcD01	D:5-33
2b	Gla-3jtcD02	D:5-33

Asymmetric Unit(hide GO term definitions)

Chain A,B (EPCR_HUMAN | Q9UNN8)

molecular function
	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:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
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:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0050819	negative regulation of coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	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:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Chain C,D (PROC_HUMAN | P04070)

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: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:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0030195	negative regulation of blood coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
	GO:0050819	negative regulation of coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation.
	GO:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
	GO:0017187	peptidyl-glutamic acid carboxylation	The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
	GO:1903142	positive regulation of establishment of endothelial barrier	Any process that activates or increases the frequency, rate or extent of establishment of endothelial barrier.
	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:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	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:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	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: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 Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CGU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PTY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:91 - Pro A:92	[ RasMol ]
		Phe B:91 - Pro B:92	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3jtc
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	EPCR_HUMAN \| Q9UNN8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	PROC_HUMAN \| P04070
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.21.69
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	176860
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	EPCR_HUMAN \| Q9UNN8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	PROC_HUMAN \| P04070
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	EPCR_HUMAN \| Q9UNN8	:	1l8j 1lqv 4v3d 4v3e
	PROC_HUMAN \| P04070	:	1aut 1lqv 1pcu 2pct 3f6u 4dt7

(no "Related Entries Specified in the PDB File" available for 3JTC)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 40)

Sites (22, 22)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

PROSITE Motifs (1, 2)

Exons (4, 7)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (34, 40)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File