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Biol. Unit 1
Info
Asym.Unit (228 KB)
Biol.Unit 1 (116 KB)
Biol.Unit 2 (111 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FRAGMENT D-DIMER FROM HUMAN FIBRIN COMPLEXED WITH GLY-HYDROXYPRO-ARG-PRO-AMIDE
Authors
:
R. F. Doolittle, J. M. Kollman, A. Chen, L. Pandi
Date
:
08 Jul 06 (Deposition) - 17 Jul 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,G (1x)
Biol. Unit 2: D,E,F,H (1x)
Keywords
:
Coiled-Coil, Knob-Hole Interactions, Blood Clotting
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
[
close entry info
]
Hetero Components
(3, 4)
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)
2a: 4-HYDROXYPROLINE (HYPa)
2b: 4-HYDROXYPROLINE (HYPb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5a: AMINO GROUP (NH2a)
5b: AMINO GROUP (NH2b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
HYP
1
Mod. Amino Acid
4-HYDROXYPROLINE
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
-1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5
NH2
1
Mod. Amino Acid
AMINO GROUP
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET B:361 , ASN B:364 , NAG B:471
BINDING SITE FOR RESIDUE NAG B 470
2
AC2
SOFTWARE
NAG B:470
BINDING SITE FOR RESIDUE NAG B 471
3
AC5
SOFTWARE
ASP B:381 , ASP B:383 , TRP B:385 , HOH B:520
BINDING SITE FOR RESIDUE CA B 2
4
AC6
SOFTWARE
ASP B:261 , GLY B:263 , ASP B:398 , GLU C:132 , HOH C:439
BINDING SITE FOR RESIDUE CA B 3
5
AC7
SOFTWARE
ASP C:318 , ASP C:320 , PHE C:322 , GLY C:324
BINDING SITE FOR RESIDUE CA C 1
6
AC8
SOFTWARE
ASP C:294 , GLY C:296 , ASP C:298 , ASP C:301
BINDING SITE FOR RESIDUE CA C 4
[
close Site info
]
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
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2hloa1 (A:126-192)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
1a
d2hloa1
A:126-192
[
close SCOP info
]
CATH Domains
(3, 10)
Info
all CATH domains
1a: CATH_2hloF01 (F:144-286,F:381-391)
1b: CATH_2hloC01 (C:144-286,C:381-393)
1c: CATH_2hloB01 (B:202-349,B:449-459)
1d: CATH_2hloE01 (E:202-349,E:449-459)
2a: CATH_2hloC02 (C:287-380)
2b: CATH_2hloB02 (B:350-448)
2c: CATH_2hloE02 (E:350-448)
2d: CATH_2hloF02 (F:287-380)
3a: CATH_2hloD00 (D:135-188)
3b: CATH_2hloA00 (A:126-192)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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
2hloF01
F:144-286,F:381-391
1b
2hloC01
C:144-286,C:381-393
1c
2hloB01
B:202-349,B:449-459
1d
2hloE01
E:202-349,E:449-459
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
2hloC02
C:287-380
2b
2hloB02
B:350-448
2c
2hloE02
E:350-448
2d
2hloF02
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
2hloD00
D:135-188
3b
2hloA00
A:126-192
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (228 KB)
Header - Asym.Unit
Biol.Unit 1 (116 KB)
Header - Biol.Unit 1
Biol.Unit 2 (111 KB)
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