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.
1MDU
Asym. Unit
Info
Asym.Unit (173 KB)
Biol.Unit 1 (248 KB)
Biol.Unit 2 (246 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE CHICKEN ACTIN TRIMER COMPLEXED WITH HUMAN GELSOLIN SEGMENT 1 (GS-1)
Authors
:
J. F. Dawson, E. P. Sablin, J. A. Spudich, R. J. Fletterick
Date
:
07 Aug 02 (Deposition) - 07 Jan 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B (3x)
Biol. Unit 2: D,E (3x)
Keywords
:
Gelsolin Precursor, A-Actin, Adenosine-5'-Triphosphate, 2- Amino-2-Hydroxymethyl-Propane-1, 3-Diol, Structural Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. F. Dawson, E. P. Sablin, J. A. Spudich, R. J. Fletterick
Structure Of An F-Actin Trimer Disrupted By Gelsolin And Implications For The Mechanism Of Severing
J. Biol. Chem. V. 278 1229 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
3a: 4-METHYL-HISTIDINE (HICa)
3b: 4-METHYL-HISTIDINE (HICb)
4a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CA
7
Ligand/Ion
CALCIUM ION
3
HIC
2
Mod. Amino Acid
4-METHYL-HISTIDINE
4
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ATP B:400 , HOH B:405 , HOH B:406 , HOH B:407 , HOH B:408 , HOH B:409
BINDING SITE FOR RESIDUE CA B 401
02
AC2
SOFTWARE
GLY A:41 , ASP A:42 , GLU A:73 , VAL A:121 , HOH A:513
BINDING SITE FOR RESIDUE CA A 402
03
AC3
SOFTWARE
ASP A:85 , GLY A:90 , ALA A:92 , HOH A:486 , HOH A:505 , GLU B:169 , HOH B:413
BINDING SITE FOR RESIDUE CA A 403
04
AC4
SOFTWARE
SER B:325 , HOH B:471 , HOH B:472 , HOH B:531 , HOH B:572 , GLU D:14
BINDING SITE FOR RESIDUE CA B 404
05
AC5
SOFTWARE
ATP E:400 , HOH E:408 , HOH E:410 , HOH E:411 , HOH E:480
BINDING SITE FOR RESIDUE CA E 401
06
AC6
SOFTWARE
GLY D:41 , ASP D:42 , GLU D:73 , VAL D:121 , HOH D:418 , HOH D:455
BINDING SITE FOR RESIDUE CA D 402
07
AC7
SOFTWARE
ASP D:85 , GLY D:90 , ALA D:92 , HOH D:425 , GLU E:169 , HOH E:403
BINDING SITE FOR RESIDUE CA D 403
08
AC8
SOFTWARE
GLY B:15 , SER B:16 , GLY B:17 , LEU B:18 , LYS B:20 , GLY B:158 , ASP B:159 , GLY B:160 , VAL B:161 , ARG B:212 , LYS B:215 , GLU B:216 , GLY B:303 , GLY B:304 , THR B:305 , MET B:307 , TYR B:308 , LYS B:338 , CA B:401 , HOH B:408 , HOH B:409 , HOH B:410 , HOH B:411 , HOH B:412 , HOH B:478 , HOH B:507 , HOH B:551
BINDING SITE FOR RESIDUE ATP B 400
09
AC9
SOFTWARE
GLY E:15 , SER E:16 , GLY E:17 , LEU E:18 , LYS E:20 , GLY E:158 , ASP E:159 , GLY E:160 , VAL E:161 , GLY E:184 , LYS E:215 , GLU E:216 , GLY E:303 , GLY E:304 , THR E:305 , MET E:307 , TYR E:308 , LYS E:338 , CA E:401 , HOH E:408 , HOH E:410 , HOH E:412 , HOH E:433 , HOH E:484
BINDING SITE FOR RESIDUE ATP E 400
10
BC1
SOFTWARE
TYR A:35 , TYR A:109 , PHE A:110 , LYS A:111 , SER A:112 , ASN E:227 , HOH E:454
BINDING SITE FOR RESIDUE TRS A 472
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024690 (A78T, chain A/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024690
A
129
T
GELS_HUMAN
Polymorphism
2230287
A/D
A
78
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: ACTINS_1 (B:55-65,E:55-65)
2: ACTINS_ACT_LIKE (B:106-118,E:106-118)
3: ACTINS_2 (B:358-366,E:358-366)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACTINS_1
PS00406
Actins signature 1.
ACTS_CHICK
55-65
2
B:55-65
E:55-65
2
ACTINS_ACT_LIKE
PS01132
Actins and actin-related proteins signature.
ACTS_CHICK
106-118
2
B:106-118
E:106-118
3
ACTINS_2
PS00432
Actins signature 2.
ACTS_CHICK
358-366
2
B:358-366
E:358-366
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.16d (A:2-66 | D:3-66)
Exon 1.17 (A:66-117 | D:66-117)
Exon 1.18b (A:118-125 | D:118-125)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.14/1.16d
2: Boundary 1.16d/1.17
3: Boundary 1.17/1.18b
4: Boundary 1.18b/1.18f
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
1.14
ENST00000373818
14
ENSE00001461665
chr9:
124062071-124062283
213
GELS_HUMAN
1-48
48
0
-
-
1.16d
ENST00000373818
16d
ENSE00001725493
chr9:
124064241-124064445
205
GELS_HUMAN
49-117
69
2
A:2-66
D:3-66
65
64
1.17
ENST00000373818
17
ENSE00001745162
chr9:
124065189-124065343
155
GELS_HUMAN
117-168
52
2
A:66-117
D:66-117
52
52
1.18b
ENST00000373818
18b
ENSE00001764209
chr9:
124072962-124073123
162
GELS_HUMAN
169-222
54
2
A:118-125
D:118-125
8
8
1.18f
ENST00000373818
18f
ENSE00001689299
chr9:
124074617-124074766
150
GELS_HUMAN
223-272
50
0
-
-
1.18i
ENST00000373818
18i
ENSE00001727906
chr9:
124076212-124076301
90
GELS_HUMAN
273-302
30
0
-
-
1.19b
ENST00000373818
19b
ENSE00001732099
chr9:
124079364-124079496
133
GELS_HUMAN
303-347
45
0
-
-
1.20
ENST00000373818
20
ENSE00001734404
chr9:
124080684-124080772
89
GELS_HUMAN
347-376
30
0
-
-
1.21a
ENST00000373818
21a
ENSE00001618926
chr9:
124080943-124081158
216
GELS_HUMAN
377-448
72
0
-
-
1.22b
ENST00000373818
22b
ENSE00001591416
chr9:
124083546-124083679
134
GELS_HUMAN
449-493
45
0
-
-
1.23
ENST00000373818
23
ENSE00001735249
chr9:
124086832-124086922
91
GELS_HUMAN
493-523
31
0
-
-
1.24a
ENST00000373818
24a
ENSE00001704432
chr9:
124088790-124088960
171
GELS_HUMAN
524-580
57
0
-
-
1.25
ENST00000373818
25
ENSE00001668309
chr9:
124089586-124089760
175
GELS_HUMAN
581-639
59
0
-
-
1.26b
ENST00000373818
26b
ENSE00001721539
chr9:
124091169-124091293
125
GELS_HUMAN
639-680
42
0
-
-
1.26c
ENST00000373818
26c
ENSE00001771020
chr9:
124091516-124091593
78
GELS_HUMAN
681-706
26
0
-
-
1.27a
ENST00000373818
27a
ENSE00001779366
chr9:
124093666-124093726
61
GELS_HUMAN
707-727
21
0
-
-
1.28d
ENST00000373818
28d
ENSE00001732346
chr9:
124094712-124095120
409
GELS_HUMAN
727-782
56
0
-
-
[
close EXON info
]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1mdua_ (A:)
1b: SCOP_d1mdud_ (D:)
2a: SCOP_d1mdub1 (B:7-146)
2b: SCOP_d1mdub2 (B:147-375)
2c: SCOP_d1mdue1 (E:7-146)
2d: SCOP_d1mdue2 (E:147-374)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Gelsolin-like
(96)
Superfamily
:
Actin depolymerizing proteins
(88)
Family
:
Gelsolin-like
(43)
Protein domain
:
Gelsolin
(33)
Human (Homo sapiens) [TaxId: 9606]
(31)
1a
d1mdua_
A:
1b
d1mdud_
D:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
Actin/HSP70
(199)
Protein domain
:
Actin
(69)
Chicken (Gallus gallus) [TaxId: 9031]
(1)
2a
d1mdub1
B:7-146
2b
d1mdub2
B:147-375
2c
d1mdue1
E:7-146
2d
d1mdue2
E:147-374
[
close SCOP info
]
CATH Domains
(4, 10)
Info
all CATH domains
1a: CATH_1mduB01 (B:8-36,B:73-136,B:339-373)
1b: CATH_1mduE01 (E:8-36,E:73-136,E:339-372)
1c: CATH_1mduB03 (B:138-183,B:273-334)
1d: CATH_1mduE03 (E:138-183,E:273-334)
2a: CATH_1mduD00 (D:3-125)
2b: CATH_1mduA00 (A:2-125)
3a: CATH_1mduB04 (B:184-269)
3b: CATH_1mduE04 (E:184-269)
4a: CATH_1mduE02 (E:37-70)
4b: CATH_1mduB02 (B:37-70)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.40, no name defined]
(217)
Human (Homo sapiens)
(36)
1a
1mduB01
B:8-36,B:73-136,B:339-373
1b
1mduE01
E:8-36,E:73-136,E:339-372
1c
1mduB03
B:138-183,B:273-334
1d
1mduE03
E:138-183,E:273-334
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Severin
(74)
Homologous Superfamily
:
Severin
(74)
Human (Homo sapiens)
(36)
2a
1mduD00
D:3-125
2b
1mduA00
A:2-125
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Actin; Chain A, domain 4
(156)
Homologous Superfamily
:
Actin; Chain A, domain 4
(155)
Human (Homo sapiens)
(29)
3a
1mduB04
B:184-269
3b
1mduE04
E:184-269
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Actin; Chain A, domain 2
(36)
Homologous Superfamily
:
Actin; Chain A, domain 2
(36)
Human (Homo sapiens)
(7)
4a
1mduE02
E:37-70
4b
1mduB02
B:37-70
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Gelsolin_1mduD01 (D:24-107)
1b: PFAM_Gelsolin_1mduD02 (D:24-107)
2a: PFAM_Actin_1mduE01 (E:7-374)
2b: PFAM_Actin_1mduE02 (E:7-374)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ADF
(44)
Family
:
Gelsolin
(23)
Homo sapiens (Human)
(13)
1a
Gelsolin-1mduD01
D:24-107
1b
Gelsolin-1mduD02
D:24-107
Clan
:
Actin_ATPase
(173)
Family
:
Actin
(70)
Gallus gallus (Chicken)
(1)
2a
Actin-1mduE01
E:7-374
2b
Actin-1mduE02
E:7-374
[
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
Chain B
Chain D
Chain E
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 (173 KB)
Header - Asym.Unit
Biol.Unit 1 (248 KB)
Header - Biol.Unit 1
Biol.Unit 2 (246 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
1MDU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help