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.
5EUL
Asym. Unit
Info
Asym.Unit (229 KB)
Biol.Unit 1 (218 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE SECA-SECY COMPLEX WITH A TRANSLOCATING POLYPEPTIDE SUBSTRATE
Authors
:
L. Li, E. Park, J. Ling, J. Ingram, H. Ploegh, T. A. Rapoport
Date
:
18 Nov 15 (Deposition) - 09 Mar 16 (Release) - 30 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.70
Chains
:
Asym. Unit : A,E,V,Y
Biol. Unit 1: A,E,V,Y (1x)
Keywords
:
Secy, Seca, Atpase, Channel, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Li, E. Park, J. Ling, J. Ingram, H. Ploegh, T. A. Rapoport
Crystal Structure Of A Substrate-Engaged Secy Protein-Translocation Channel.
Nature V. 531 395 2016
[
close entry info
]
Hetero Components
(4, 21)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2a: BERYLLIUM TRIFLUORIDE ION (BEFa)
3a: MAGNESIUM ION (MGa)
4a: HEXATANTALUM DODECABROMIDE (TBRa)
4b: HEXATANTALUM DODECABROMIDE (TBRb)
4c: HEXATANTALUM DODECABROMIDE (TBRc)
4d: HEXATANTALUM DODECABROMIDE (TBRd)
4e: HEXATANTALUM DODECABROMIDE (TBRe)
4f: HEXATANTALUM DODECABROMIDE (TBRf)
4g: HEXATANTALUM DODECABROMIDE (TBRg)
4h: HEXATANTALUM DODECABROMIDE (TBRh)
4i: HEXATANTALUM DODECABROMIDE (TBRi)
4j: HEXATANTALUM DODECABROMIDE (TBRj)
4k: HEXATANTALUM DODECABROMIDE (TBRk)
4l: HEXATANTALUM DODECABROMIDE (TBRl)
4m: HEXATANTALUM DODECABROMIDE (TBRm)
4n: HEXATANTALUM DODECABROMIDE (TBRn)
4o: HEXATANTALUM DODECABROMIDE (TBRo)
4p: HEXATANTALUM DODECABROMIDE (TBRp)
4q: HEXATANTALUM DODECABROMIDE (TBRq)
4r: HEXATANTALUM DODECABROMIDE (TBRr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
BEF
1
Ligand/Ion
BERYLLIUM TRIFLUORIDE ION
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
TBR
18
Ligand/Ion
HEXATANTALUM DODECABROMIDE
[
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ADP A:1003
binding site for residue MG A 1001
02
AC2
SOFTWARE
THR A:102 , GLY A:103 , ASP A:492 , ADP A:1003
binding site for residue BEF A 1002
03
AC3
SOFTWARE
MET A:79 , PHE A:80 , PHE A:82 , GLN A:85 , GLY A:103 , GLY A:105 , LYS A:106 , THR A:107 , LEU A:108 , ASP A:492 , ARG A:528 , GLN A:529 , MG A:1001 , BEF A:1002
binding site for residue ADP A 1003
04
AC4
SOFTWARE
ASP A:591 , GLN A:595 , GLN A:598 , TYR A:599 , GLU Y:103 , ARG Y:106
binding site for residue TBR A 1004
05
AC5
SOFTWARE
GLU A:798 , MET A:801 , GLU A:802 , PRO Y:263
binding site for residue TBR A 1005
06
AC6
SOFTWARE
THR A:251 , ASP A:253 , THR A:256 , VAL A:298 , ALA A:299 , MET A:300 , GLU A:544 , ARG A:547
binding site for residue TBR A 1006
07
AC7
SOFTWARE
LYS A:302 , ASP A:303 , GLU A:443 , LYS A:447 , LYS A:462
binding site for residue TBR A 1007
08
AC8
SOFTWARE
HIS A:43 , GLU A:47 , GLU A:50
binding site for residue TBR A 1008
09
AC9
SOFTWARE
THR A:120 , HIS A:202 , ASP A:276 , GLU A:365 , LYS A:366
binding site for residue TBR A 1009
10
AD1
SOFTWARE
GLU A:625 , GLU A:628 , ASN A:629 , MET A:689 , ILE A:693
binding site for residue TBR A 1010
11
AD2
SOFTWARE
LYS A:723 , ASP A:726 , HIS A:809 , SER A:813
binding site for residue TBR A 1011
12
AD3
SOFTWARE
ASP A:773 , GLU A:778 , GLU A:780 , SER Y:289 , ARG Y:301 , ARG Y:302
binding site for residue TBR A 1012
13
AD4
SOFTWARE
LYS A:229 , LYS A:232 , TYR A:234 , ALA A:285 , HIS A:288 , HIS A:289 , GLU A:348
binding site for residue TBR A 1013
14
AD5
SOFTWARE
GLU A:309 , ASP A:310 , LYS A:325 , LYS A:462 , HIS A:464 , GLU A:465
binding site for residue TBR A 1014
15
AD6
SOFTWARE
GLU A:443 , SER A:446 , LYS A:450 , VAL A:458
binding site for residue TBR A 1015
16
AD7
SOFTWARE
GLU A:34 , GLU A:71 , ARG A:74 , ARG A:75
binding site for residue TBR A 1016
17
AD8
SOFTWARE
THR A:376 , GLU A:379 , LYS A:583 , GLU A:586 , PHE A:590 , MET Y:104 , ARG Y:107
binding site for residue TBR A 1017
18
AD9
SOFTWARE
ARG A:14 , GLU A:378 , GLU A:379 , GLN A:388
binding site for residue TBR A 1018
19
AE1
SOFTWARE
GLU A:50 , GLU A:53 , PRO Y:242
binding site for residue TBR Y 501
20
AE2
SOFTWARE
PHE A:804 , GLU Y:417
binding site for residue TBR Y 502
21
AE3
SOFTWARE
ARG A:553 , LYS Y:94 , GLU Y:97
binding site for residue TBR Y 503
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain E
Chain V
Chain Y
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 (229 KB)
Header - Asym.Unit
Biol.Unit 1 (218 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
5EUL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help