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.
PLEASE WAIT...
Getting 'Exon' information from database.
3FIB
Asym. Unit
Info
Asym.Unit (48 KB)
Biol.Unit 1 (45 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) BOUND TO CALCIUM AT PH 6.0: A FURTHER REFINEMENT OF PDB ENTRY 1FIB, AND DIFFERS FROM 1FIB BY THE MODELLING OF A CIS PEPTIDE BOND BETWEEN RESIDUES K338 AND C339
Authors
:
K. P. Pratt, H. C. F. Cote, D. W. Chung, R. E. Stenkamp, E. W. Davie
Date
:
14 Jul 97 (Deposition) - 17 Sep 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Fibrinogen, Blood Coagulation, Fibrin Polymerization, Cis Peptide Bonds
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. P. Pratt, H. C. Cote, D. W. Chung, R. E. Stenkamp, E. W. Davie
The Primary Fibrin Polymerization Pocket: Three-Dimensional Structure Of A 30-Kda C-Terminal Gamma Chain Fragment Complexed With The Peptide Gly-Pro-Arg-Pro.
Proc. Natl. Acad. Sci. Usa V. 94 7176 1997
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:318 , ASP A:320 , PHE A:322 , GLY A:324 , HOH A:401 , HOH A:402
BINDING SITE FOR RESIDUE CA A 400
[
close Site info
]
SAPs(SNPs)/Variants
(20, 20)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_014170 (G165R, chain A, )
02: VAR_002409 (R275C, chain A, )
03: VAR_002410 (R275H, chain A, )
04: VAR_072726 (T277P, chain A, )
05: VAR_002411 (G292V, chain A, )
06: VAR_072727 (D301H, chain A, )
07: VAR_002413 (N308I, chain A, )
08: VAR_002412 (N308K, chain A, )
09: VAR_015853 (G309D, chain A, )
10: VAR_002414 (M310T, chain A, )
11: VAR_072728 (N319D, chain A, )
12: VAR_002416 (Q329R, chain A, )
13: VAR_002418 (D330V, chain A, )
14: VAR_002417 (D330Y, chain A, )
15: VAR_002419 (N337K, chain A, )
16: VAR_002421 (S358C, chain A, )
17: VAR_002422 (R375G, chain A, )
18: VAR_072729 (R375W, chain A, )
19: VAR_072621 (S378P, chain A, )
20: VAR_014171 (M384V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_014170
G
191
R
FIBG_HUMAN
Polymorphism
6063
A
G
165
R
02
UniProt
VAR_002409
R
301
C
FIBG_HUMAN
Unclassified
---
A
R
275
C
03
UniProt
VAR_002410
R
301
H
FIBG_HUMAN
Disease (DYSFIBRIN)
---
A
R
275
H
04
UniProt
VAR_072726
T
303
P
FIBG_HUMAN
Disease (CAFBN)
---
A
T
277
P
05
UniProt
VAR_002411
G
318
V
FIBG_HUMAN
Disease (DYSFIBRIN)
---
A
G
292
V
06
UniProt
VAR_072727
D
327
H
FIBG_HUMAN
Disease (CAFBN)
---
A
D
301
H
07
UniProt
VAR_002413
N
334
I
FIBG_HUMAN
Polymorphism
121913090
A
N
308
I
08
UniProt
VAR_002412
N
334
K
FIBG_HUMAN
Unclassified
---
A
N
308
K
09
UniProt
VAR_015853
G
335
D
FIBG_HUMAN
Unclassified
---
A
G
309
D
10
UniProt
VAR_002414
M
336
T
FIBG_HUMAN
Unclassified
---
A
M
310
T
11
UniProt
VAR_072728
N
345
D
FIBG_HUMAN
Disease (CAFBN)
---
A
N
319
D
12
UniProt
VAR_002416
Q
355
R
FIBG_HUMAN
Unclassified
---
A
Q
329
R
13
UniProt
VAR_002418
D
356
V
FIBG_HUMAN
Disease (DYSFIBRIN)
---
A
D
330
V
14
UniProt
VAR_002417
D
356
Y
FIBG_HUMAN
Unclassified
---
A
D
330
Y
15
UniProt
VAR_002419
N
363
K
FIBG_HUMAN
Unclassified
---
A
N
337
K
16
UniProt
VAR_002421
S
384
C
FIBG_HUMAN
Unclassified
---
A
S
358
C
17
UniProt
VAR_002422
R
401
G
FIBG_HUMAN
Unclassified
---
A
R
375
G
18
UniProt
VAR_072729
R
401
W
FIBG_HUMAN
Disease (CAFBN)
---
A
R
375
W
19
UniProt
VAR_072621
S
404
P
FIBG_HUMAN
Disease (DYSFIBRIN)
---
A
S
378
P
20
UniProt
VAR_014171
M
410
V
FIBG_HUMAN
Polymorphism
6061
A
M
384
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: FIBRINOGEN_C_2 (A:144-390)
2: FIBRINOGEN_C_1 (A: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
A:144-390
2
FIBRINOGEN_C_1
PS00514
Fibrinogen C-terminal domain signature.
FIBG_HUMAN
360-372
1
A:334-346
[
close PROSITE info
]
Exons
(5, 5)
Info
All Exons
Exon 1.3a (A:144-152)
Exon 1.3f (A:152-196)
Exon 1.4b (A:197-258)
Exon 1.5 (A:258-351)
Exon 1.6c (A:351-392)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2g/1.3a
2: Boundary 1.3a/1.3f
3: Boundary 1.3f/1.4b
4: Boundary 1.4b/1.5
5: Boundary 1.5/1.6c
6: Boundary 1.6c/-
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
1.1f
ENST00000336098
1f
ENSE00001820766
chr4:
155533800-155533684
117
FIBG_HUMAN
1-26
26
0
-
-
1.2a
ENST00000336098
2a
ENSE00001781463
chr4:
155533587-155533543
45
FIBG_HUMAN
27-41
15
0
-
-
1.2d
ENST00000336098
2d
ENSE00001624767
chr4:
155533353-155533170
184
FIBG_HUMAN
42-103
62
0
-
-
1.2g
ENST00000336098
2g
ENSE00001652916
chr4:
155533050-155532957
94
FIBG_HUMAN
103-134
32
0
-
-
1.3a
ENST00000336098
3a
ENSE00001127239
chr4:
155531349-155531219
131
FIBG_HUMAN
134-178
45
1
A:144-152
9
1.3f
ENST00000336098
3f
ENSE00002146570
chr4:
155530915-155530782
134
FIBG_HUMAN
178-222
45
1
A:152-196
45
1.4b
ENST00000336098
4b
ENSE00001127220
chr4:
155529802-155529618
185
FIBG_HUMAN
223-284
62
1
A:197-258
62
1.5
ENST00000336098
5
ENSE00001127212
chr4:
155528134-155527857
278
FIBG_HUMAN
284-377
94
1
A:258-351
94
1.6c
ENST00000336098
6c
ENSE00001344514
chr4:
155526218-155525728
491
FIBG_HUMAN
377-453
77
1
A:351-392
42
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3fiba_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
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), gamma [TaxId: 9606]
(21)
1a
d3fiba_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3fibA01 (A:144-286,A:381-391)
2a: CATH_3fibA02 (A:287-380)
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
3fibA01
A:144-286,A: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
3fibA02
A:287-380
[
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 A
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 (48 KB)
Header - Asym.Unit
Biol.Unit 1 (45 KB)
Header - Biol.Unit 1
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
3FIB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
