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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1OKK
Asym. Unit
Info
Asym.Unit (109 KB)
Biol.Unit 1 (102 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HOMO-HETERODIMERIC COMPLEX OF THE SRP GTPASES
Authors
:
P. J. Focia, D. M. Freymann
Date
:
26 Jul 03 (Deposition) - 19 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,D
Biol. Unit 1: A,D (1x)
Keywords
:
Cell Cycle, Signal Recognition/Complex, Srp, Ffh, Ftsy, Gtpase, Membrane Targeting, Signal Sequence Recognition
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. J. Focia, I. V. Shepotinovskaya, J. A. Seidler, D. M. Freymann
Heterodimeric Gtpase Core Of The Srp Targeting Complex
Science V. 303 373 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 21)
Info
All Hetero Components
1a: N1-CARBOXYPIPERAZINE (BZPa)
1b: N1-CARBOXYPIPERAZINE (BZPb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
3a: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (GCPa)
3b: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (GCPb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BZP
2
Ligand/Ion
N1-CARBOXYPIPERAZINE
2
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
3
GCP
2
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
SO4
11
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:21 , HOH A:2344 , HOH A:2345 , HOH A:2346 , HOH A:2347 , VAL D:160 , ILE D:161 , GLN D:162 , HOH D:2102
BINDING SITE FOR RESIDUE SO4 A1298
02
AC2
SOFTWARE
ARG A:32 , ARG A:35 , ARG A:49 , HOH A:2349
BINDING SITE FOR RESIDUE SO4 A1299
03
AC3
SOFTWARE
ALA A:140 , ALA A:141 , ARG A:142 , GLU A:143 , HOH A:2202
BINDING SITE FOR RESIDUE SO4 A1300
04
AC4
SOFTWARE
LYS A:28 , ARG A:286 , ARG A:290 , HOH A:2350 , HOH A:2351 , HOH A:2352
BINDING SITE FOR RESIDUE SO4 A1301
05
AC5
SOFTWARE
SER A:67 , LEU A:68 , THR A:69 , HOH A:2353 , HOH A:2354 , LYS D:132 , ARG D:183 , TYR D:185
BINDING SITE FOR RESIDUE SO4 A1302
06
AC6
SOFTWARE
SER A:164 , SER A:167 , ARG A:170 , HOH A:2355
BINDING SITE FOR RESIDUE SO4 A1303
07
AC7
SOFTWARE
ARG A:128 , ARG A:181
BINDING SITE FOR RESIDUE SO4 A1304
08
AC8
SOFTWARE
ARG A:169 , ARG A:170 , HOH A:2356
BINDING SITE FOR RESIDUE SO4 A1305
09
AC9
SOFTWARE
ARG A:231 , HOH A:2357 , LYS D:207 , ARG D:211
BINDING SITE FOR RESIDUE SO4 A1306
10
BC1
SOFTWARE
ARG A:142 , MET A:160 , ASP A:161
BINDING SITE FOR RESIDUE SO4 A1307
11
BC2
SOFTWARE
ARG D:124 , ARG D:155 , PRO D:286 , HOH D:2209
BINDING SITE FOR RESIDUE SO4 D1308
12
BC3
SOFTWARE
THR A:112 , GCP A:1001 , HOH A:2196 , HOH A:2207 , HOH A:2249
BINDING SITE FOR RESIDUE MG A1002
13
BC4
SOFTWARE
THR D:116 , GCP D:1001 , HOH D:2082 , HOH D:2123 , HOH D:2207
BINDING SITE FOR RESIDUE MG D1002
14
BC5
SOFTWARE
GLN A:107 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , THR A:113 , LYS A:117 , ASP A:135 , ARG A:138 , GLN A:144 , GLY A:190 , LYS A:246 , ASP A:248 , GLY A:271 , VAL A:272 , SER A:273 , GLU A:274 , MG A:1002 , HOH A:2181 , HOH A:2182 , HOH A:2196 , HOH A:2197 , HOH A:2207 , HOH A:2249 , HOH A:2342 , ASN D:111 , ARG D:142 , LEU D:196 , GCP D:1001 , HOH D:2065
BINDING SITE FOR RESIDUE GCP A1001
15
BC6
SOFTWARE
ALA A:270 , GLU A:280 , PRO A:281 , PHE A:282 , TYR A:283 , ARG A:286 , ARG A:290
BINDING SITE FOR RESIDUE BZP A1296
16
BC7
SOFTWARE
LYS A:96 , ASP A:97 , ARG A:98 , LYS A:206 , HOH A:2175
BINDING SITE FOR RESIDUE BZP A1297
17
BC8
SOFTWARE
GLN A:107 , ARG A:138 , GCP A:1001 , ASN D:111 , GLY D:112 , VAL D:113 , GLY D:114 , LYS D:115 , THR D:116 , THR D:117 , LYS D:121 , ARG D:142 , GLN D:148 , GLY D:194 , LYS D:256 , ASP D:258 , GLY D:281 , VAL D:282 , GLY D:283 , GLU D:284 , MG D:1002 , HOH D:2067 , HOH D:2082 , HOH D:2085 , HOH D:2123 , HOH D:2207 , HOH D:2208
BINDING SITE FOR RESIDUE GCP D1001
18
BC9
SOFTWARE
LEU A:106 , GLN A:193 , VAL D:231 , GLY D:259 , THR D:260 , ALA D:261 , HOH D:2172
BINDING SITE FOR RESIDUE EDO D1309
19
CC1
SOFTWARE
ARG A:127 , LYS D:215 , EDO D:1311
BINDING SITE FOR RESIDUE EDO D1310
20
CC2
SOFTWARE
TYR D:174 , LYS D:215 , EDO D:1310
BINDING SITE FOR RESIDUE EDO D1311
21
CC3
SOFTWARE
GLU D:151 , TRP D:152 , ARG D:155 , HOH D:2210 , HOH D:2211
BINDING SITE FOR RESIDUE EDO D1312
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: SRP54 (A:266-279,D:276-289)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SRP54
PS00300
SRP54-type proteins GTP-binding domain signature.
SRP54_THEAQ
266-279
1
A:266-279
FTSY_THEAQ
276-289
1
D:276-289
[
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.
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1okkd1 (D:21-78)
2a: SCOP_d1okka1 (A:4-88)
3a: SCOP_d1okkd2 (D:97-303)
4a: SCOP_d1okka2 (A:89-293)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Domain of the SRP/SRP receptor G-proteins
(34)
Family
:
Domain of the SRP/SRP receptor G-proteins
(29)
Protein domain
:
Signal recognition particle receptor, FtsY
(7)
Thermus aquaticus [TaxId: 271]
(4)
1a
d1okkd1
D:21-78
Protein domain
:
Signal sequence recognition protein Ffh
(21)
Thermus aquaticus [TaxId: 271]
(17)
2a
d1okka1
A:4-88
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Nitrogenase iron protein-like
(152)
Protein domain
:
GTPase domain of the signal recognition particle receptor FtsY
(7)
Thermus aquaticus [TaxId: 271]
(4)
3a
d1okkd2
D:97-303
Protein domain
:
GTPase domain of the signal sequence recognition protein Ffh
(21)
Thermus aquaticus [TaxId: 271]
(17)
4a
d1okka2
A:89-293
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1okkA02 (A:91-281)
1b: CATH_1okkD02 (D:97-303)
2a: CATH_1okkA01 (A:4-90)
2b: CATH_1okkD01 (D:21-78)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Thermus aquaticus. Organism_taxid: 271.
(14)
1a
1okkA02
A:91-281
1b
1okkD02
D:97-303
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.140, no name defined]
(15)
Thermus aquaticus. Organism_taxid: 271.
(6)
2a
1okkA01
A:4-90
2b
1okkD01
D:21-78
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_SRP54_1okkD01 (D:102-303)
1b: PFAM_SRP54_1okkA01 (A:98-293)
2a: PFAM_SRP54_N_1okkD02 (D:21-77)
2b: PFAM_SRP54_N_1okkA02 (A:5-82)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
SRP54
(20)
Thermus aquaticus
(12)
1a
SRP54-1okkD01
D:102-303
1b
SRP54-1okkA01
A:98-293
Clan
:
no clan defined [family: SRP54_N]
(20)
Family
:
SRP54_N
(20)
Thermus aquaticus
(12)
2a
SRP54_N-1okkD02
D:21-77
2b
SRP54_N-1okkA02
A:5-82
[
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 D
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 (109 KB)
Header - Asym.Unit
Biol.Unit 1 (102 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
1OKK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
