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1LQV
Asym. Unit
Info
Asym.Unit (96 KB)
Biol.Unit 1 (46 KB)
Biol.Unit 2 (44 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ENDOTHELIAL PROTEIN C RECEPTOR WITH PHOSPHOLIPID IN THE GROOVE IN COMPLEX WITH GLA DOMAIN OF PROTEIN C.
Authors
:
V. Oganesyan, N. Oganesyan, S. Terzyan, Q. Dongfeng, Z. Dauter, N. L. Es C. T. Esmon
Date
:
13 May 02 (Deposition) - 19 Jun 02 (Release) - 13 Jul 11 (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
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Oganesyan, N. Oganesyan, S. Terzyan, D. Qu, Z. Dauter, N. L. Esmon, C. T. Esmon
The Crystal Structure Of The Endothelial Protein C Receptor And A Bound Phospholipid.
J. Biol. Chem. V. 277 24851 2002
[
close entry info
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Hetero Components
(5, 40)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
2a: GAMMA-CARBOXY-GLUTAMIC ACID (CGUa)
2b: GAMMA-CARBOXY-GLUTAMIC ACID (CGUb)
2c: GAMMA-CARBOXY-GLUTAMIC ACID (CGUc)
2d: GAMMA-CARBOXY-GLUTAMIC ACID (CGUd)
2e: GAMMA-CARBOXY-GLUTAMIC ACID (CGUe)
2f: GAMMA-CARBOXY-GLUTAMIC ACID (CGUf)
2g: GAMMA-CARBOXY-GLUTAMIC ACID (CGUg)
2h: GAMMA-CARBOXY-GLUTAMIC ACID (CGUh)
2i: GAMMA-CARBOXY-GLUTAMIC ACID (CGUi)
2j: GAMMA-CARBOXY-GLUTAMIC ACID (CGUj)
2k: GAMMA-CARBOXY-GLUTAMIC ACID (CGUk)
2l: GAMMA-CARBOXY-GLUTAMIC ACID (CGUl)
2m: GAMMA-CARBOXY-GLUTAMIC ACID (CGUm)
2n: GAMMA-CARBOXY-GLUTAMIC ACID (CGUn)
2o: GAMMA-CARBOXY-GLUTAMIC ACID (CGUo)
2p: GAMMA-CARBOXY-GLUTAMIC ACID (CGUp)
2q: GAMMA-CARBOXY-GLUTAMIC ACID (CGUq)
2r: GAMMA-CARBOXY-GLUTAMIC ACID (CGUr)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5a: PHOSPHATIDYLETHANOLAMINE (PTYa)
5b: PHOSPHATIDYLETHANOLAMINE (PTYb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
14
Ligand/Ion
CALCIUM ION
2
CGU
18
Mod. Amino Acid
GAMMA-CARBOXY-GLUTAMIC ACID
3
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5
PTY
2
Ligand/Ion
PHOSPHATIDYLETHANOLAMINE
[
close Hetero Component info
]
Sites
(22, 22)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
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
02
AC2
SOFTWARE
ALA B:90 , PRO B:92 , ASN B:119 , HOH B:626 , HOH B:701
BINDING SITE FOR RESIDUE NAG B 601
03
AC3
SOFTWARE
ASN B:155 , HOH B:660 , HOH B:686
BINDING SITE FOR RESIDUE NAG B 602
04
AC4
SOFTWARE
LEU A:14 , ILE A:16 , ASN A:30 , ARG A:96 , HOH A:785
BINDING SITE FOR RESIDUE NAG A 603
05
AC5
SOFTWARE
ALA A:90 , PRO A:92 , ASN A:119 , HOH A:729
BINDING SITE FOR RESIDUE NAG A 604
06
AC6
SOFTWARE
ASN A:155
BINDING SITE FOR RESIDUE NDG A 605
07
AC7
SOFTWARE
GLU A:86 , CGU C:7 , CGU C:26 , CGU C:29 , HOH C:47
BINDING SITE FOR RESIDUE CA C 34
08
AC8
SOFTWARE
GLU A:86 , HOH A:615 , CGU C:25 , CGU C:29
BINDING SITE FOR RESIDUE CA C 35
09
AC9
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
10
BC1
SOFTWARE
GLU B:86 , CGU D:7 , CGU D:26 , CGU D:29 , HOH D:54
BINDING SITE FOR RESIDUE CA D 37
11
BC2
SOFTWARE
ALA D:1 , CGU D:6 , CGU D:16 , CGU D:20 , HOH D:77
BINDING SITE FOR RESIDUE CA D 38
12
BC3
SOFTWARE
CGU D:14 , CGU D:19 , HOH D:68 , HOH D:87
BINDING SITE FOR RESIDUE CA D 39
13
BC4
SOFTWARE
GLU B:86 , HOH B:658 , CGU D:25 , CGU D:29
BINDING SITE FOR RESIDUE CA D 40
14
BC5
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 41
15
BC6
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 42
16
BC7
SOFTWARE
CGU C:20 , HOH C:63 , HOH C:66 , HOH C:79 , HOH C:80
BINDING SITE FOR RESIDUE CA C 43
17
BC8
SOFTWARE
CGU D:20 , HOH D:58 , HOH D:69 , HOH D:70 , HOH D:75
BINDING SITE FOR RESIDUE CA D 44
18
BC9
SOFTWARE
ALA C:1 , CGU C:6 , CGU C:16 , CGU C:20 , HOH C:59
BINDING SITE FOR RESIDUE CA C 45
19
CC1
SOFTWARE
CGU C:14 , CGU C:19 , HOH C:67 , HOH C:99
BINDING SITE FOR RESIDUE CA C 46
20
CC2
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 47
21
CC3
SOFTWARE
LEU A:14 , ASN A:30 , HIS A:39 , LEU A:41 , LEU A:69 , TYR A:72 , PHE A:76 , PHE A:123 , ARG A:156 , THR A:157 , GLU A:160 , PHE A:164 , THR A:168 , CYS A:169 , HOH A:700 , HOH A:701 , HOH A:702
BINDING SITE FOR RESIDUE PTY A 606
22
CC4
SOFTWARE
LEU B:14 , 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 , THR B:168 , CYS B:169 , TYR B:172 , HOH B:638 , HOH B:642 , HOH B:679 , HOH B:714
BINDING SITE FOR RESIDUE PTY B 607
[
close Site info
]
SAPs(SNPs)/Variants
(7, 14)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_006639 (A1T, chain C/D, )
2: VAR_006640 (E7D, chain C/D, )
3: VAR_006641 (R9C, chain C/D, )
4: VAR_006643 (R15G, chain C/D, )
5: VAR_006644 (R15Q, chain C/D, )
6: VAR_006642 (R15W, chain C/D, )
7: VAR_006645 (E20A, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006639
A
43
T
PROC_HUMAN
Polymorphism
---
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
Unclassified
---
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
Unclassified
---
C/D
R
15
Q
6
UniProt
VAR_006642
R
57
W
PROC_HUMAN
Disease (THPH3)
---
C/D
R
15
W
7
UniProt
VAR_006645
E
62
A
PROC_HUMAN
Disease (THPH3)
---
C/D
E
20
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: GLA_1 (C:16-33,D:16-33)
;
View:
Select:
Label:
End label:
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
[
close PROSITE info
]
Exons
(4, 7)
Info
All Exons
Exon 1.3a (A:7-7 | -)
Exon 1.4 (A:7-91 | B:8-91)
Exon 1.5 (A:91-178 | B:91-180)
Exon 2.3a (C:1-33 | D:1-33)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.3a
2: Boundary 1.3a/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6a
5: Boundary 2.2e/2.3a
6: Boundary 2.3a/2.4a
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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
-
-
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1lqva_ (A:)
1b: SCOP_d1lqvb_ (B:)
2a: SCOP_d1lqvc_ (C:)
2b: SCOP_d1lqvd_ (D:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Endothelial protein C receptor
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1lqva_
A:
1b
d1lqvb_
B:
Class
:
Small proteins
(3458)
Fold
:
GLA-domain
(44)
Superfamily
:
GLA-domain
(44)
Family
:
GLA-domain
(37)
Protein domain
:
Coagulation factor XIV (Protein C)
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d1lqvc_
C:
2b
d1lqvd_
D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1lqvB00 (B:8-180)
1b: CATH_1lqvA00 (A:7-178)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
(402)
Homologous Superfamily
:
Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1
(400)
Human (Homo sapiens)
(249)
1a
1lqvB00
B:8-180
1b
1lqvA00
A:7-178
[
close CATH info
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_MHC_I_1lqvB01 (B:53-180)
1b: PFAM_MHC_I_1lqvB02 (B:53-180)
2a: PFAM_Gla_1lqvD01 (D:5-33)
2b: PFAM_Gla_1lqvD02 (D:5-33)
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Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
1a
MHC_I-1lqvB01
B:53-180
1b
MHC_I-1lqvB02
B:53-180
Clan
:
no clan defined [family: Gla]
(24)
Family
:
Gla
(24)
Homo sapiens (Human)
(14)
2a
Gla-1lqvD01
D:5-33
2b
Gla-1lqvD02
D:5-33
[
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