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2Q9I
Asym. Unit
Info
Asym.Unit (207 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (101 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D-DIMER FROM HUMAN FIBRIN COMPLEXED WITH MET-HIS-ARG-PRO-TYR-AMIDE.
Authors
:
R. F. Doolittle, L. Pandi
Date
:
12 Jun 07 (Deposition) - 11 Dec 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,M,N,S,T
Biol. Unit 1: A,B,C,M,S (1x)
Biol. Unit 2: D,E,F,N,T (1x)
Keywords
:
Fibrin Clots, B-Knobs, Beta-Holes, Blood Coagulation, Disease Mutation, Glycoprotein, Phosphoprotein, Secreted, Pyrrolidone Carboxylic Acid, Blood Clotting
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. F. Doolittle, L. Pandi
Probing The Beta-Chain Hole Of Fibrinogen With Synthetic Peptides That Differ At Their Amino Termini
Biochemistry V. 46 10033 2007
[
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Hetero Components
(2, 12)
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)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(31, 62)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_033930 (Y114H, chain C/F, )
02: VAR_002399 (R141S, chain A/D, )
03: VAR_014170 (G165R, chain C/F, )
04: VAR_072723 (C165W, chain A/D, )
05: VAR_016908 (R166C, chain B/E, )
06: VAR_072620 (L172Q, chain B/E, )
07: VAR_013093 (P235L, chain B/E, )
08: VAR_002409 (R275C, chain C/F, )
09: VAR_002410 (R275H, chain C/F, )
10: VAR_072726 (T277P, chain C/F, )
11: VAR_002411 (G292V, chain C/F, )
12: VAR_072727 (D301H, chain C/F, )
13: VAR_002413 (N308I, chain C/F, )
14: VAR_002412 (N308K, chain C/F, )
15: VAR_015853 (G309D, chain C/F, )
16: VAR_002414 (M310T, chain C/F, )
17: VAR_072728 (N319D, chain C/F, )
18: VAR_002416 (Q329R, chain C/F, )
19: VAR_002418 (D330V, chain C/F, )
20: VAR_002417 (D330Y, chain C/F, )
21: VAR_002407 (A335T, chain B/E, )
22: VAR_002419 (N337K, chain C/F, )
23: VAR_016909 (L353R, chain B/E, )
24: VAR_002421 (S358C, chain C/F, )
25: VAR_002422 (R375G, chain C/F, )
26: VAR_072729 (R375W, chain C/F, )
27: VAR_072725 (T377K, chain B/E, )
28: VAR_072621 (S378P, chain C/F, )
29: VAR_014171 (M384V, chain C/F, )
30: VAR_016910 (G400D, chain B/E, )
31: VAR_002408 (R448K, chain B/E, )
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/F
Y
114
H
02
UniProt
VAR_002399
R
160
S
FIBA_HUMAN
Unclassified
---
A/D
R
141
S
03
UniProt
VAR_014170
G
191
R
FIBG_HUMAN
Polymorphism
6063
C/F
G
165
R
04
UniProt
VAR_072723
C
184
W
FIBA_HUMAN
Disease (CAFBN)
---
A/D
C
165
W
05
UniProt
VAR_016908
R
196
C
FIBB_HUMAN
Disease (CAFBN)
---
B/E
R
166
C
06
UniProt
VAR_072620
L
202
Q
FIBB_HUMAN
Disease (CAFBN)
---
B/E
L
172
Q
07
UniProt
VAR_013093
P
265
L
FIBB_HUMAN
Polymorphism
6054
B/E
P
235
L
08
UniProt
VAR_002409
R
301
C
FIBG_HUMAN
Unclassified
---
C/F
R
275
C
09
UniProt
VAR_002410
R
301
H
FIBG_HUMAN
Disease (DYSFIBRIN)
---
C/F
R
275
H
10
UniProt
VAR_072726
T
303
P
FIBG_HUMAN
Disease (CAFBN)
---
C/F
T
277
P
11
UniProt
VAR_002411
G
318
V
FIBG_HUMAN
Disease (DYSFIBRIN)
---
C/F
G
292
V
12
UniProt
VAR_072727
D
327
H
FIBG_HUMAN
Disease (CAFBN)
---
C/F
D
301
H
13
UniProt
VAR_002413
N
334
I
FIBG_HUMAN
Polymorphism
121913090
C/F
N
308
I
14
UniProt
VAR_002412
N
334
K
FIBG_HUMAN
Unclassified
---
C/F
N
308
K
15
UniProt
VAR_015853
G
335
D
FIBG_HUMAN
Unclassified
---
C/F
G
309
D
16
UniProt
VAR_002414
M
336
T
FIBG_HUMAN
Unclassified
---
C/F
M
310
T
17
UniProt
VAR_072728
N
345
D
FIBG_HUMAN
Disease (CAFBN)
---
C/F
N
319
D
18
UniProt
VAR_002416
Q
355
R
FIBG_HUMAN
Unclassified
---
C/F
Q
329
R
19
UniProt
VAR_002418
D
356
V
FIBG_HUMAN
Disease (DYSFIBRIN)
---
C/F
D
330
V
20
UniProt
VAR_002417
D
356
Y
FIBG_HUMAN
Unclassified
---
C/F
D
330
Y
21
UniProt
VAR_002407
A
365
T
FIBB_HUMAN
Unclassified
---
B/E
A
335
T
22
UniProt
VAR_002419
N
363
K
FIBG_HUMAN
Unclassified
---
C/F
N
337
K
23
UniProt
VAR_016909
L
383
R
FIBB_HUMAN
Disease (CAFBN)
---
B/E
L
353
R
24
UniProt
VAR_002421
S
384
C
FIBG_HUMAN
Unclassified
---
C/F
S
358
C
25
UniProt
VAR_002422
R
401
G
FIBG_HUMAN
Unclassified
---
C/F
R
375
G
26
UniProt
VAR_072729
R
401
W
FIBG_HUMAN
Disease (CAFBN)
---
C/F
R
375
W
27
UniProt
VAR_072725
T
407
K
FIBB_HUMAN
Disease (CAFBN)
---
B/E
T
377
K
28
UniProt
VAR_072621
S
404
P
FIBG_HUMAN
Disease (DYSFIBRIN)
---
C/F
S
378
P
29
UniProt
VAR_014171
M
410
V
FIBG_HUMAN
Polymorphism
6061
C/F
M
384
V
30
UniProt
VAR_016910
G
430
D
FIBB_HUMAN
Disease (CAFBN)
---
B/E
G
400
D
31
UniProt
VAR_002408
R
478
K
FIBB_HUMAN
Polymorphism
4220
B/E
R
448
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: FIBRINOGEN_C_2 (C:144-390,F:144-390,B:202-458,E:20...)
2: FIBRINOGEN_C_1 (C:334-346,F:334-346,B:402-414,E:40...)
;
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
2
C:144-390
F:144-390
FIBB_HUMAN
232-488
2
B:202-458
E:202-458
2
FIBRINOGEN_C_1
PS00514
Fibrinogen C-terminal domain signature.
FIBG_HUMAN
360-372
2
C:334-346
F:334-346
FIBB_HUMAN
432-444
2
B:402-414
E:402-414
[
close PROSITE info
]
Exons
(13, 25)
Info
All Exons
Exon 1.4b (A:126-151 | D:135-151)
Exon 1.5b (A:152-192 | D:152-188)
Exon 2.4b (B:157-210 | E:164-210)
Exon 2.5 (B:210-248 | E:210-248)
Exon 2.6 (B:248-290 | E:248-290)
Exon 2.7 (B:290-385 | E:290-385)
Exon 2.8c (B:385-459 | E:385-459)
Exon 3.2g (C:102-108 | -)
Exon 3.3a (C:108-152 | F:109-152)
Exon 3.3f (C:152-196 | F:152-196)
Exon 3.4b (C:197-258 | F:197-258)
Exon 3.5 (C:258-351 | F:258-351)
Exon 3.6c (C:351-393 | F:351-393)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3/1.4b
02: Boundary 1.4b/1.5b
03: Boundary 1.5b/1.6
04: Boundary 2.3b/2.4b
05: Boundary 2.4b/2.5
06: Boundary 2.5/2.6
07: Boundary 2.6/2.7
08: Boundary 2.7/2.8c
09: Boundary 2.8c/-
10: Boundary 3.2d/3.2g
11: Boundary 3.2g/3.3a
12: Boundary 3.3a/3.3f
13: Boundary 3.3f/3.4b
14: Boundary 3.4b/3.5
15: Boundary 3.5/3.6c
16: Boundary 3.6c/-
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
1.1a
ENST00000302053
1a
ENSE00001909776
chr4:
155511918-155511786
133
FIBA_HUMAN
1-18
18
0
-
-
1.2
ENST00000302053
2
ENSE00001127292
chr4:
155510714-155510589
126
FIBA_HUMAN
19-60
42
0
-
-
1.3
ENST00000302053
3
ENSE00001127283
chr4:
155510128-155509945
184
FIBA_HUMAN
61-122
62
0
-
-
1.4b
ENST00000302053
4b
ENSE00001127274
chr4:
155508809-155508664
146
FIBA_HUMAN
122-170
49
2
A:126-151
D:135-151
26
17
1.5b
ENST00000302053
5b
ENSE00001127263
chr4:
155508070-155506690
1381
FIBA_HUMAN
171-631
461
2
A:152-192
D:152-188
41
37
1.6
ENST00000302053
6
ENSE00001210975
chr4:
155505985-155504278
1708
FIBA_HUMAN
631-866
236
0
-
-
2.1a
ENST00000302068
1a
ENSE00001171218
chr4:
155484108-155484284
177
FIBB_HUMAN
1-38
38
0
-
-
2.2d
ENST00000302068
2d
ENSE00001640255
chr4:
155486960-155487151
192
FIBB_HUMAN
39-102
64
0
-
-
2.3b
ENST00000302068
3b
ENSE00001645081
chr4:
155487641-155487824
184
FIBB_HUMAN
103-164
62
0
-
-
2.4b
ENST00000302068
4b
ENSE00001127321
chr4:
155488745-155488972
228
FIBB_HUMAN
164-240
77
2
B:157-210
E:164-210
54
47
2.5
ENST00000302068
5
ENSE00001127313
chr4:
155489533-155489646
114
FIBB_HUMAN
240-278
39
2
B:210-248
E:210-248
39
39
2.6
ENST00000302068
6
ENSE00001127308
chr4:
155490334-155490459
126
FIBB_HUMAN
278-320
43
2
B:248-290
E:248-290
43
43
2.7
ENST00000302068
7
ENSE00001127300
chr4:
155490666-155490951
286
FIBB_HUMAN
320-415
96
2
B:290-385
E:290-385
96
96
2.8c
ENST00000302068
8c
ENSE00001171210
chr4:
155491571-155492238
668
FIBB_HUMAN
415-491
77
2
B:385-459
E:385-459
75
75
3.1f
ENST00000336098
1f
ENSE00001820766
chr4:
155533800-155533684
117
FIBG_HUMAN
1-26
26
0
-
-
3.2a
ENST00000336098
2a
ENSE00001781463
chr4:
155533587-155533543
45
FIBG_HUMAN
27-41
15
0
-
-
3.2d
ENST00000336098
2d
ENSE00001624767
chr4:
155533353-155533170
184
FIBG_HUMAN
42-103
62
0
-
-
3.2g
ENST00000336098
2g
ENSE00001652916
chr4:
155533050-155532957
94
FIBG_HUMAN
103-134
32
1
C:102-108
-
7
-
3.3a
ENST00000336098
3a
ENSE00001127239
chr4:
155531349-155531219
131
FIBG_HUMAN
134-178
45
2
C:108-152
F:109-152
45
44
3.3f
ENST00000336098
3f
ENSE00002146570
chr4:
155530915-155530782
134
FIBG_HUMAN
178-222
45
2
C:152-196
F:152-196
45
45
3.4b
ENST00000336098
4b
ENSE00001127220
chr4:
155529802-155529618
185
FIBG_HUMAN
223-284
62
2
C:197-258
F:197-258
62
62
3.5
ENST00000336098
5
ENSE00001127212
chr4:
155528134-155527857
278
FIBG_HUMAN
284-377
94
2
C:258-351
F:258-351
94
94
3.6c
ENST00000336098
6c
ENSE00001344514
chr4:
155526218-155525728
491
FIBG_HUMAN
377-453
77
2
C:351-393
F:351-393
43
43
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(3, 10)
Info
all CATH domains
1a: CATH_2q9iF01 (F:144-286,F:381-391)
1b: CATH_2q9iC01 (C:144-286,C:381-393)
1c: CATH_2q9iB01 (B:202-349,B:449-459)
1d: CATH_2q9iE01 (E:202-349,E:449-459)
2a: CATH_2q9iC02 (C:287-380)
2b: CATH_2q9iF02 (F:287-380)
2c: CATH_2q9iB02 (B:350-448)
2d: CATH_2q9iE02 (E:350-448)
3a: CATH_2q9iD00 (D:135-188)
3b: CATH_2q9iA00 (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
2q9iF01
F:144-286,F:381-391
1b
2q9iC01
C:144-286,C:381-393
1c
2q9iB01
B:202-349,B:449-459
1d
2q9iE01
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
2q9iC02
C:287-380
2b
2q9iF02
F:287-380
2c
2q9iB02
B:350-448
2d
2q9iE02
E:350-448
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
2q9iD00
D:135-188
3b
2q9iA00
A:126-192
[
close CATH info
]
Pfam Domains
(2, 10)
Info
all PFAM domains
1a: PFAM_Fibrinogen_C_2q9iE01 (E:207-457)
1b: PFAM_Fibrinogen_C_2q9iE02 (E:207-457)
1c: PFAM_Fibrinogen_C_2q9iF01 (F:149-389)
1d: PFAM_Fibrinogen_C_2q9iF02 (F:149-389)
2a: PFAM_Fib_alpha_2q9iD01 (D:135-175)
2b: PFAM_Fib_alpha_2q9iD02 (D:135-175)
2c: PFAM_Fib_alpha_2q9iE03 (E:164-205)
2d: PFAM_Fib_alpha_2q9iE04 (E:164-205)
2e: PFAM_Fib_alpha_2q9iF03 (F:109-147)
2f: PFAM_Fib_alpha_2q9iF04 (F:109-147)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Fibrinogen_C
(23)
Family
:
Fibrinogen_C
(23)
Homo sapiens (Human)
(19)
1a
Fibrinogen_C-2q9iE01
E:207-457
1b
Fibrinogen_C-2q9iE02
E:207-457
1c
Fibrinogen_C-2q9iF01
F:149-389
1d
Fibrinogen_C-2q9iF02
F:149-389
Clan
:
no clan defined [family: Fib_alpha]
(17)
Family
:
Fib_alpha
(17)
Homo sapiens (Human)
(12)
2a
Fib_alpha-2q9iD01
D:135-175
2b
Fib_alpha-2q9iD02
D:135-175
2c
Fib_alpha-2q9iE03
E:164-205
2d
Fib_alpha-2q9iE04
E:164-205
2e
Fib_alpha-2q9iF03
F:109-147
2f
Fib_alpha-2q9iF04
F:109-147
[
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Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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