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1RF1
Biol. Unit 1
Info
Asym.Unit (230 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (114 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FRAGMENT D OF GAMMAE132A FIBRINOGEN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE
Authors
:
M. S. Kostelansky, O. V. Gorkun, S. T. Lord
Date
:
07 Nov 03 (Deposition) - 16 Mar 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.53
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,G,H (1x)
Biol. Unit 2: D,E,F,I,J (1x)
Keywords
:
Blood Coagulation, Fibrinogen, Fibrinogen Fragment D, Recombinant Fibrinogen Fragment D, Fragment D Of Gammae132A, Fibrinogen With Ghrp-Amide, Blood Clotting
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. S. Kostelansky, K. C. Lounes, L. F. Ping, S. K. Dickerson, O. V. Gorkun, S. T. Lord
Calcium-Binding Site Beta2, Adjacent To The "B" Polymerization Site, Modulates Lateral Aggregation Of Protofibrils During Fibrin Polymerization.
Biochemistry V. 43 2475 2004
[
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
NAG B:4 , FUC B:5 , MET B:361 , ASN B:364 , HIS H:2 , PRO H:4
BINDING SITE FOR RESIDUE NAG B 3
2
AC2
SOFTWARE
NAG B:3 , FUC B:5
BINDING SITE FOR RESIDUE NAG B 4
3
AC3
SOFTWARE
NAG B:3 , NAG B:4 , HIS H:2
BINDING SITE FOR RESIDUE FUC B 5
4
AC7
SOFTWARE
ASP B:381 , ASP B:383 , TRP B:385 , HOH B:471
BINDING SITE FOR RESIDUE CA B 462
5
AC8
SOFTWARE
ASP C:318 , ASP C:320 , PHE C:322 , GLY C:324
BINDING SITE FOR RESIDUE CA C 407
[
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]
SAPs(SNPs)/Variants
(31, 31)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_033930 (Y114H, chain C, )
02: VAR_002399 (R141S, chain A, )
03: VAR_014170 (G165R, chain C, )
04: VAR_072723 (C165W, chain A, )
05: VAR_016908 (R166C, chain B, )
06: VAR_072620 (L172Q, chain B, )
07: VAR_013093 (P235L, chain B, )
08: VAR_002409 (R275C, chain C, )
09: VAR_002410 (R275H, chain C, )
10: VAR_072726 (T277P, chain C, )
11: VAR_002411 (G292V, chain C, )
12: VAR_072727 (D301H, chain C, )
13: VAR_002413 (N308I, chain C, )
14: VAR_002412 (N308K, chain C, )
15: VAR_015853 (G309D, chain C, )
16: VAR_002414 (M310T, chain C, )
17: VAR_072728 (N319D, chain C, )
18: VAR_002416 (Q329R, chain C, )
19: VAR_002418 (D330V, chain C, )
20: VAR_002417 (D330Y, chain C, )
21: VAR_002407 (A335T, chain B, )
22: VAR_002419 (N337K, chain C, )
23: VAR_016909 (L353R, chain B, )
24: VAR_002421 (S358C, chain C, )
25: VAR_002422 (R375G, chain C, )
26: VAR_072729 (R375W, chain C, )
27: VAR_072725 (T377K, chain B, )
28: VAR_072621 (S378P, chain C, )
29: VAR_014171 (M384V, chain C, )
30: VAR_016910 (G400D, chain B, )
31: VAR_002408 (R448K, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_033930
Y
140
H
FIBG_HUMAN
Polymorphism
2066870
C
Y
114
H
02
UniProt
VAR_002399
R
160
S
FIBA_HUMAN
Unclassified
---
A
R
141
S
03
UniProt
VAR_014170
G
191
R
FIBG_HUMAN
Polymorphism
6063
C
G
165
R
04
UniProt
VAR_072723
C
184
W
FIBA_HUMAN
Disease (CAFBN)
---
A
C
165
W
05
UniProt
VAR_016908
R
196
C
FIBB_HUMAN
Disease (CAFBN)
---
B
R
166
C
06
UniProt
VAR_072620
L
202
Q
FIBB_HUMAN
Disease (CAFBN)
---
B
L
172
Q
07
UniProt
VAR_013093
P
265
L
FIBB_HUMAN
Polymorphism
6054
B
P
235
L
08
UniProt
VAR_002409
R
301
C
FIBG_HUMAN
Unclassified
---
C
R
275
C
09
UniProt
VAR_002410
R
301
H
FIBG_HUMAN
Disease (DYSFIBRIN)
---
C
R
275
H
10
UniProt
VAR_072726
T
303
P
FIBG_HUMAN
Disease (CAFBN)
---
C
T
277
P
11
UniProt
VAR_002411
G
318
V
FIBG_HUMAN
Disease (DYSFIBRIN)
---
C
G
292
V
12
UniProt
VAR_072727
D
327
H
FIBG_HUMAN
Disease (CAFBN)
---
C
D
301
H
13
UniProt
VAR_002413
N
334
I
FIBG_HUMAN
Polymorphism
121913090
C
N
308
I
14
UniProt
VAR_002412
N
334
K
FIBG_HUMAN
Unclassified
---
C
N
308
K
15
UniProt
VAR_015853
G
335
D
FIBG_HUMAN
Unclassified
---
C
G
309
D
16
UniProt
VAR_002414
M
336
T
FIBG_HUMAN
Unclassified
---
C
M
310
T
17
UniProt
VAR_072728
N
345
D
FIBG_HUMAN
Disease (CAFBN)
---
C
N
319
D
18
UniProt
VAR_002416
Q
355
R
FIBG_HUMAN
Unclassified
---
C
Q
329
R
19
UniProt
VAR_002418
D
356
V
FIBG_HUMAN
Disease (DYSFIBRIN)
---
C
D
330
V
20
UniProt
VAR_002417
D
356
Y
FIBG_HUMAN
Unclassified
---
C
D
330
Y
21
UniProt
VAR_002407
A
365
T
FIBB_HUMAN
Unclassified
---
B
A
335
T
22
UniProt
VAR_002419
N
363
K
FIBG_HUMAN
Unclassified
---
C
N
337
K
23
UniProt
VAR_016909
L
383
R
FIBB_HUMAN
Disease (CAFBN)
---
B
L
353
R
24
UniProt
VAR_002421
S
384
C
FIBG_HUMAN
Unclassified
---
C
S
358
C
25
UniProt
VAR_002422
R
401
G
FIBG_HUMAN
Unclassified
---
C
R
375
G
26
UniProt
VAR_072729
R
401
W
FIBG_HUMAN
Disease (CAFBN)
---
C
R
375
W
27
UniProt
VAR_072725
T
407
K
FIBB_HUMAN
Disease (CAFBN)
---
B
T
377
K
28
UniProt
VAR_072621
S
404
P
FIBG_HUMAN
Disease (DYSFIBRIN)
---
C
S
378
P
29
UniProt
VAR_014171
M
410
V
FIBG_HUMAN
Polymorphism
6061
C
M
384
V
30
UniProt
VAR_016910
G
430
D
FIBB_HUMAN
Disease (CAFBN)
---
B
G
400
D
31
UniProt
VAR_002408
R
478
K
FIBB_HUMAN
Polymorphism
4220
B
R
448
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: FIBRINOGEN_C_2 (C:144-390)
2: FIBRINOGEN_C_1 (C:334-346)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FIBRINOGEN_C_2
PS51406
Fibrinogen C-terminal domain profile.
FIBG_HUMAN
170-416
1
C:144-390
-
FIBB_HUMAN
232-488
1
B:202-458
-
2
FIBRINOGEN_C_1
PS00514
Fibrinogen C-terminal domain signature.
FIBG_HUMAN
360-372
1
C:334-346
-
FIBB_HUMAN
432-444
1
B:402-414
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d1rf1b1 (B:200-459)
1b: SCOP_d1rf1e1 (E:200-459)
2a: SCOP_d1rf1c1 (C:142-393)
2b: SCOP_d1rf1f1 (F:142-393)
3a: SCOP_d1rf1a_ (A:)
3b: SCOP_d1rf1d_ (D:)
4a: SCOP_d1rf1b2 (B:161-199)
4b: SCOP_d1rf1e2 (E:165-199)
5a: SCOP_d1rf1c2 (C:96-141)
5b: SCOP_d1rf1f2 (F:103-141)
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
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)
Human (Homo sapiens), beta [TaxId: 9606]
(14)
1a
d1rf1b1
B:200-459
1b
d1rf1e1
E:200-459
Human (Homo sapiens), gamma [TaxId: 9606]
(21)
2a
d1rf1c1
C:142-393
2b
d1rf1f1
F:142-393
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)
Human (Homo sapiens) [TaxId: 9606]
(22)
3a
d1rf1a_
A:
3b
d1rf1d_
D:
Protein domain
:
Fibrinogen beta chain
(20)
Human (Homo sapiens) [TaxId: 9606]
(15)
4a
d1rf1b2
B:161-199
4b
d1rf1e2
E:165-199
Protein domain
:
Fibrinogen gamma chain
(23)
Human (Homo sapiens) [TaxId: 9606]
(18)
5a
d1rf1c2
C:96-141
5b
d1rf1f2
F:103-141
[
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]
CATH Domains
(3, 14)
Info
all CATH domains
1a: CATH_1rf1C02 (C:144-286,C:381-391)
1b: CATH_1rf1B02 (B:202-349,B:449-459)
1c: CATH_1rf1E02 (E:202-349,E:449-459)
1d: CATH_1rf1F02 (F:144-286,F:381-391)
2a: CATH_1rf1C03 (C:287-380)
2b: CATH_1rf1B03 (B:350-448)
2c: CATH_1rf1E03 (E:350-448)
2d: CATH_1rf1F03 (F:287-380)
3a: CATH_1rf1A00 (A:127-190)
3b: CATH_1rf1D00 (D:133-188)
3c: CATH_1rf1B01 (B:161-201)
3d: CATH_1rf1C01 (C:96-143)
3e: CATH_1rf1F01 (F:103-143)
3f: CATH_1rf1E01 (E:165-201)
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Classes
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)
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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)
Human (Homo sapiens)
(53)
1a
1rf1C02
C:144-286,C:381-391
1b
1rf1B02
B:202-349,B:449-459
1c
1rf1E02
E:202-349,E:449-459
1d
1rf1F02
F:144-286,F:381-391
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)
Human (Homo sapiens)
(53)
2a
1rf1C03
C:287-380
2b
1rf1B03
B:350-448
2c
1rf1E03
E:350-448
2d
1rf1F03
F:287-380
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)
Human (Homo sapiens)
(28)
3a
1rf1A00
A:127-190
3b
1rf1D00
D:133-188
3c
1rf1B01
B:161-201
3d
1rf1C01
C:96-143
3e
1rf1F01
F:103-143
3f
1rf1E01
E:165-201
[
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Pfam Domains
(2, 10)
Info
all PFAM domains
1a: PFAM_Fibrinogen_C_1rf1E01 (E:207-457)
1b: PFAM_Fibrinogen_C_1rf1E02 (E:207-457)
1c: PFAM_Fibrinogen_C_1rf1F01 (F:149-389)
1d: PFAM_Fibrinogen_C_1rf1F02 (F:149-389)
2a: PFAM_Fib_alpha_1rf1D01 (D:133-175)
2b: PFAM_Fib_alpha_1rf1D02 (D:133-175)
2c: PFAM_Fib_alpha_1rf1E03 (E:165-205)
2d: PFAM_Fib_alpha_1rf1E04 (E:165-205)
2e: PFAM_Fib_alpha_1rf1F03 (F:103-147)
2f: PFAM_Fib_alpha_1rf1F04 (F:103-147)
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Clans
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Families
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(
)
Organisms
(
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(
)
Clan
:
Fibrinogen_C
(23)
Family
:
Fibrinogen_C
(23)
Homo sapiens (Human)
(19)
1a
Fibrinogen_C-1rf1E01
E:207-457
1b
Fibrinogen_C-1rf1E02
E:207-457
1c
Fibrinogen_C-1rf1F01
F:149-389
1d
Fibrinogen_C-1rf1F02
F:149-389
Clan
:
no clan defined [family: Fib_alpha]
(17)
Family
:
Fib_alpha
(17)
Homo sapiens (Human)
(12)
2a
Fib_alpha-1rf1D01
D:133-175
2b
Fib_alpha-1rf1D02
D:133-175
2c
Fib_alpha-1rf1E03
E:165-205
2d
Fib_alpha-1rf1E04
E:165-205
2e
Fib_alpha-1rf1F03
F:103-147
2f
Fib_alpha-1rf1F04
F:103-147
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