PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2FFD
Biol. Unit 2
Info
Asym.Unit (226 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (110 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FIBRINOGEN FRAGMENT D WITH "A" KNOB PEPTIDE MIMIC GPRVVE
Authors
:
L. Betts
Date
:
19 Dec 05 (Deposition) - 04 Jul 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.89
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,G,J (1x)
Biol. Unit 2: D,E,F,H,I (1x)
Keywords
:
Complex Of Fibrinogen With "A" Site Mimic Gprvve In Both "A" And "B" Sites, Blood Clotting
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Betts, B. K. Merenbloom, S. T. Lord
The Structure Of Fibrinogen Fragment D With The 'A' Knob Peptide Gprvve.
Thromb. Haemost. V. 4 1139 2006
[
close entry info
]
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
]
Sites
(5, 5)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
NAG E:4 , FUC E:5 , MET E:361 , ASN E:364
BINDING SITE FOR RESIDUE NAG E 3
2
AC5
SOFTWARE
NAG E:3 , FUC E:5
BINDING SITE FOR RESIDUE NAG E 4
3
AC6
SOFTWARE
NAG E:3 , NAG E:4
BINDING SITE FOR RESIDUE FUC E 5
4
AC9
SOFTWARE
ASP E:381 , ASP E:383 , TRP E:385
BINDING SITE FOR RESIDUE CA E 602
5
BC1
SOFTWARE
ASP F:318 , ASP F:320 , PHE F:322 , GLY F:324 , HOH F:627
BINDING SITE FOR RESIDUE CA F 603
[
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 F, )
02: VAR_002399 (R141S, chain D, )
03: VAR_014170 (G165R, chain F, )
04: VAR_072723 (C165W, chain D, )
05: VAR_016908 (R166C, chain E, )
06: VAR_072620 (L172Q, chain E, )
07: VAR_013093 (P235L, chain E, )
08: VAR_002409 (R275C, chain F, )
09: VAR_002410 (R275H, chain F, )
10: VAR_072726 (T277P, chain F, )
11: VAR_002411 (G292V, chain F, )
12: VAR_072727 (D301H, chain F, )
13: VAR_002413 (N308I, chain F, )
14: VAR_002412 (N308K, chain F, )
15: VAR_015853 (G309D, chain F, )
16: VAR_002414 (M310T, chain F, )
17: VAR_072728 (N319D, chain F, )
18: VAR_002416 (Q329R, chain F, )
19: VAR_002418 (D330V, chain F, )
20: VAR_002417 (D330Y, chain F, )
21: VAR_002407 (A335T, chain E, )
22: VAR_002419 (N337K, chain F, )
23: VAR_016909 (L353R, chain E, )
24: VAR_002421 (S358C, chain F, )
25: VAR_002422 (R375G, chain F, )
26: VAR_072729 (R375W, chain F, )
27: VAR_072725 (T377K, chain E, )
28: VAR_072621 (S378P, chain F, )
29: VAR_014171 (M384V, chain F, )
30: VAR_016910 (G400D, chain E, )
31: VAR_002408 (R448K, chain 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
F
Y
114
H
02
UniProt
VAR_002399
R
160
S
FIBA_HUMAN
Unclassified
---
D
R
141
S
03
UniProt
VAR_014170
G
191
R
FIBG_HUMAN
Polymorphism
6063
F
G
165
R
04
UniProt
VAR_072723
C
184
W
FIBA_HUMAN
Disease (CAFBN)
---
D
C
165
W
05
UniProt
VAR_016908
R
196
C
FIBB_HUMAN
Disease (CAFBN)
---
E
R
166
C
06
UniProt
VAR_072620
L
202
Q
FIBB_HUMAN
Disease (CAFBN)
---
E
L
172
Q
07
UniProt
VAR_013093
P
265
L
FIBB_HUMAN
Polymorphism
6054
E
P
235
L
08
UniProt
VAR_002409
R
301
C
FIBG_HUMAN
Unclassified
---
F
R
275
C
09
UniProt
VAR_002410
R
301
H
FIBG_HUMAN
Disease (DYSFIBRIN)
---
F
R
275
H
10
UniProt
VAR_072726
T
303
P
FIBG_HUMAN
Disease (CAFBN)
---
F
T
277
P
11
UniProt
VAR_002411
G
318
V
FIBG_HUMAN
Disease (DYSFIBRIN)
---
F
G
292
V
12
UniProt
VAR_072727
D
327
H
FIBG_HUMAN
Disease (CAFBN)
---
F
D
301
H
13
UniProt
VAR_002413
N
334
I
FIBG_HUMAN
Polymorphism
121913090
F
N
308
I
14
UniProt
VAR_002412
N
334
K
FIBG_HUMAN
Unclassified
---
F
N
308
K
15
UniProt
VAR_015853
G
335
D
FIBG_HUMAN
Unclassified
---
F
G
309
D
16
UniProt
VAR_002414
M
336
T
FIBG_HUMAN
Unclassified
---
F
M
310
T
17
UniProt
VAR_072728
N
345
D
FIBG_HUMAN
Disease (CAFBN)
---
F
N
319
D
18
UniProt
VAR_002416
Q
355
R
FIBG_HUMAN
Unclassified
---
F
Q
329
R
19
UniProt
VAR_002418
D
356
V
FIBG_HUMAN
Disease (DYSFIBRIN)
---
F
D
330
V
20
UniProt
VAR_002417
D
356
Y
FIBG_HUMAN
Unclassified
---
F
D
330
Y
21
UniProt
VAR_002407
A
365
T
FIBB_HUMAN
Unclassified
---
E
A
335
T
22
UniProt
VAR_002419
N
363
K
FIBG_HUMAN
Unclassified
---
F
N
337
K
23
UniProt
VAR_016909
L
383
R
FIBB_HUMAN
Disease (CAFBN)
---
E
L
353
R
24
UniProt
VAR_002421
S
384
C
FIBG_HUMAN
Unclassified
---
F
S
358
C
25
UniProt
VAR_002422
R
401
G
FIBG_HUMAN
Unclassified
---
F
R
375
G
26
UniProt
VAR_072729
R
401
W
FIBG_HUMAN
Disease (CAFBN)
---
F
R
375
W
27
UniProt
VAR_072725
T
407
K
FIBB_HUMAN
Disease (CAFBN)
---
E
T
377
K
28
UniProt
VAR_072621
S
404
P
FIBG_HUMAN
Disease (DYSFIBRIN)
---
F
S
378
P
29
UniProt
VAR_014171
M
410
V
FIBG_HUMAN
Polymorphism
6061
F
M
384
V
30
UniProt
VAR_016910
G
430
D
FIBB_HUMAN
Disease (CAFBN)
---
E
G
400
D
31
UniProt
VAR_002408
R
478
K
FIBB_HUMAN
Polymorphism
4220
E
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 (F:144-390)
2: FIBRINOGEN_C_1 (F: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
-
F:144-390
FIBB_HUMAN
232-488
1
-
E:202-458
2
FIBRINOGEN_C_1
PS00514
Fibrinogen C-terminal domain signature.
FIBG_HUMAN
360-372
1
-
F:334-346
FIBB_HUMAN
432-444
1
-
E:402-414
[
close PROSITE info
]
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2ffda1 (A:126-190)
1b: SCOP_d2ffdd1 (D:133-189)
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
d2ffda1
A:126-190
1b
d2ffdd1
D:133-189
[
close SCOP info
]
CATH Domains
(3, 14)
Info
all CATH domains
1a: CATH_2ffdC02 (C:144-286,C:381-391)
1b: CATH_2ffdF02 (F:144-286,F:381-391)
1c: CATH_2ffdB02 (B:202-349,B:449-459)
1d: CATH_2ffdE02 (E:202-349,E:449-459)
2a: CATH_2ffdC03 (C:287-380)
2b: CATH_2ffdF03 (F:287-380)
2c: CATH_2ffdB03 (B:350-448)
2d: CATH_2ffdE03 (E:350-448)
3a: CATH_2ffdA00 (A:126-190)
3b: CATH_2ffdD00 (D:133-189)
3c: CATH_2ffdB01 (B:157-201)
3d: CATH_2ffdC01 (C:96-143)
3e: CATH_2ffdF01 (F:110-143)
3f: CATH_2ffdE01 (E:165-201)
View:
Select:
Label:
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
2ffdC02
C:144-286,C:381-391
1b
2ffdF02
F:144-286,F:381-391
1c
2ffdB02
B:202-349,B:449-459
1d
2ffdE02
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
2ffdC03
C:287-380
2b
2ffdF03
F:287-380
2c
2ffdB03
B:350-448
2d
2ffdE03
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
2ffdA00
A:126-190
3b
2ffdD00
D:133-189
3c
2ffdB01
B:157-201
3d
2ffdC01
C:96-143
3e
2ffdF01
F:110-143
3f
2ffdE01
E:165-201
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain D
Chain E
Chain F
Chain H
Chain I
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
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)
[
close Script example commands
]
Log
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (226 KB)
Header - Asym.Unit
Biol.Unit 1 (114 KB)
Header - Biol.Unit 1
Biol.Unit 2 (110 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2FFD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help