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1N73
Asym. Unit
Info
Asym.Unit (250 KB)
Biol.Unit 1 (244 KB)
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(1)
Title
:
FIBRIN D-DIMER, LAMPREY COMPLEXED WITH THE PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE
Authors
:
Z. Yang, L. Pandi, R. F. Doolittle
Date
:
12 Nov 02 (Deposition) - 07 Jan 03 (Release) - 08 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Isopeptide Cross-Linked Chains; Protein-Peptide Complex, Blood Clotting
(Keyword Search:
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Reference
:
Z. Yang, L. Pandi, R. F. Doolittle
The Crystal Structure Of Fragment Double-D From Cross-Linke Lamprey Fibrin Reveals Isopeptide Linkages Across An Unexpected D-D Interface
Biochemistry V. 41 15610 2002
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET B:381 , ASN B:384
BINDING SITE FOR RESIDUE NAG B 480
2
AC2
SOFTWARE
MET E:381 , ASN E:384 , HIS J:2
BINDING SITE FOR RESIDUE NAG E 480
3
AC3
SOFTWARE
ASN C:203
BINDING SITE FOR RESIDUE NAG C 480
4
AC4
SOFTWARE
ASN F:203
BINDING SITE FOR RESIDUE NAG F 480
5
AC5
SOFTWARE
ASP C:316 , ASP C:318 , TYR C:320 , GLY C:322
BINDING SITE FOR RESIDUE CA C 1
6
AC6
SOFTWARE
ASP F:316 , ASP F:318 , TYR F:320 , GLY F:322
BINDING SITE FOR RESIDUE CA F 2
7
AC7
SOFTWARE
ASP B:401 , ASP B:403 , TRP B:405 , ASN B:406 , LYS B:412
BINDING SITE FOR RESIDUE CA B 3
8
AC8
SOFTWARE
ASP E:401 , ASP E:403 , TRP E:405 , ASN E:406 , LYS E:412
BINDING SITE FOR RESIDUE CA E 4
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: FIBRINOGEN_C_2 (C:145-388,F:145-388,B:223-477,E:22...)
2: FIBRINOGEN_C_1 (C:332-344,F:332-344,B:422-434,E:42...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FIBRINOGEN_C_2
PS51406
Fibrinogen C-terminal domain profile.
FIBG_PETMA
169-412
2
C:145-388
F:145-388
FIBB_PETMA
221-476
2
B:223-477
E:223-477
2
FIBRINOGEN_C_1
PS00514
Fibrinogen C-terminal domain signature.
FIBG_PETMA
356-368
2
C:332-344
F:332-344
FIBB_PETMA
420-432
2
B:422-434
E:422-434
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d1n73b1 (B:219-477)
1b: SCOP_d1n73e1 (E:219-477)
2a: SCOP_d1n73c1 (C:138-404)
2b: SCOP_d1n73f1 (F:138-404)
3a: SCOP_d1n73a_ (A:)
3b: SCOP_d1n73d_ (D:)
4a: SCOP_d1n73b2 (B:163-218)
4b: SCOP_d1n73e2 (E:163-218)
5a: SCOP_d1n73c2 (C:83-137)
5b: SCOP_d1n73f2 (F:83-137)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Fibrinogen C-terminal domain-like
(70)
Superfamily
:
Fibrinogen C-terminal domain-like
(70)
Family
:
Fibrinogen C-terminal domain-like
(43)
Protein domain
:
Fibrinogen C-terminal domains
(42)
Sea lamprey (Petromyzon marinus), beta [TaxId: 7757]
(2)
1a
d1n73b1
B:219-477
1b
d1n73e1
E:219-477
Sea lamprey (Petromyzon marinus), gamma [TaxId: 7757]
(2)
2a
d1n73c1
C:138-404
2b
d1n73f1
F:138-404
Class
:
Coiled coil proteins
(689)
Fold
:
Parallel coiled-coil
(407)
Superfamily
:
Fibrinogen coiled-coil and central regions
(71)
Family
:
Fibrinogen coiled-coil and central regions
(70)
Protein domain
:
Fibrinogen alpha chain
(27)
Sea lamprey (Petromyzon marinus) [TaxId: 7757]
(2)
3a
d1n73a_
A:
3b
d1n73d_
D:
Protein domain
:
Fibrinogen beta chain
(20)
Sea lamprey (Petromyzon marinus) [TaxId: 7757]
(2)
4a
d1n73b2
B:163-218
4b
d1n73e2
E:163-218
Protein domain
:
Fibrinogen gamma chain
(23)
Sea lamprey (Petromyzon marinus) [TaxId: 7757]
(2)
5a
d1n73c2
C:83-137
5b
d1n73f2
F:83-137
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CATH Domains
(3, 14)
Info
all CATH domains
1a: CATH_1n73C01 (C:145-284,C:379-389)
1b: CATH_1n73B01 (B:223-369,B:469-477)
1c: CATH_1n73E01 (E:223-369,E:469-477)
1d: CATH_1n73F01 (F:145-284,F:379-389)
2a: CATH_1n73C02 (C:285-378)
2b: CATH_1n73B02 (B:370-468)
2c: CATH_1n73E02 (E:370-468)
2d: CATH_1n73F02 (F:285-378)
3a: CATH_1n73C03 (C:83-144)
3b: CATH_1n73B03 (B:163-222)
3c: CATH_1n73E03 (E:163-222)
3d: CATH_1n73D00 (D:101-190)
3e: CATH_1n73A00 (A:103-193)
3f: CATH_1n73F03 (F:83-144)
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Gamma Fibrinogen; Chain A, domain 1
(58)
Homologous Superfamily
:
Gamma Fibrinogen, chain A, domain 1
(58)
Sea lamprey (Petromyzon marinus)
(2)
1a
1n73C01
C:145-284,C:379-389
1b
1n73B01
B:223-369,B:469-477
1c
1n73E01
E:223-369,E:469-477
1d
1n73F01
F:145-284,F:379-389
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
(58)
Homologous Superfamily
:
Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
(58)
Sea lamprey (Petromyzon marinus)
(2)
2a
1n73C02
C:285-378
2b
1n73B02
B:370-468
2c
1n73E02
E:370-468
2d
1n73F02
F:285-378
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.50, no name defined]
(33)
Sea lamprey (Petromyzon marinus)
(2)
3a
1n73C03
C:83-144
3b
1n73B03
B:163-222
3c
1n73E03
E:163-222
3d
1n73D00
D:101-190
3e
1n73A00
A:103-193
3f
1n73F03
F:83-144
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Fibrinogen_C_1n73F01 (F:150-387)
1b: PFAM_Fibrinogen_C_1n73F02 (F:150-387)
2a: PFAM_Fib_alpha_1n73D01 (D:101-167)
2b: PFAM_Fib_alpha_1n73D02 (D:101-167)
2c: PFAM_Fib_alpha_1n73F03 (F:83-148)
2d: PFAM_Fib_alpha_1n73F04 (F:83-148)
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Clans
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Clan
:
Fibrinogen_C
(23)
Family
:
Fibrinogen_C
(23)
Petromyzon marinus (Sea lamprey)
(2)
1a
Fibrinogen_C-1n73F01
F:150-387
1b
Fibrinogen_C-1n73F02
F:150-387
Clan
:
no clan defined [family: Fib_alpha]
(17)
Family
:
Fib_alpha
(17)
Petromyzon marinus (Sea lamprey)
(2)
2a
Fib_alpha-1n73D01
D:101-167
2b
Fib_alpha-1n73D02
D:101-167
2c
Fib_alpha-1n73F03
F:83-148
2d
Fib_alpha-1n73F04
F:83-148
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