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.
5F0J
Asym. Unit
Info
Asym.Unit (165 KB)
Biol.Unit 1 (158 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 RETROMER VPS26-VPS35 SUBUNITS BOUND TO SNX3
Authors
:
M. Lucas, D. Gershlick, A. Vidaurrazaga, A. L. Rojas, J. S. Bonifacino,
Date
:
27 Nov 15 (Deposition) - 07 Dec 16 (Release) - 14 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Protein Transport, Retromer, Sorting Nexin, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Lucas, D. C. Gershlick, A. Vidaurrazaga, A. L. Rojas, J. S. Bonifacino, A. Hierro
Structural Mechanism For Cargo Recognition By The Retromer Complex.
Cell V. 167 1623 2016
[
close entry info
]
Hetero Components
(4, 43)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
1v: 1,2-ETHANEDIOL (EDOv)
1w: 1,2-ETHANEDIOL (EDOw)
1x: 1,2-ETHANEDIOL (EDOx)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
24
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
5
Ligand/Ion
GLYCEROL
3
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
4
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:54
binding site for residue SO4 A 501
02
AC2
SOFTWARE
ALA A:101 , GLY A:102 , HOH A:607
binding site for residue SO4 A 502
03
AC3
SOFTWARE
LYS A:38 , LEU A:39 , MET A:40 , ASP A:41
binding site for residue GOL A 503
04
AC4
SOFTWARE
ARG A:54 , ILE A:105 , GLU B:234 , ASP B:237
binding site for residue EDO A 504
05
AC5
SOFTWARE
GLN A:155 , ARG A:158 , ARG A:226 , GLN A:229
binding site for residue EDO A 505
06
AC6
SOFTWARE
CYS A:137 , VAL A:140 , GLN A:141 , ARG A:150 , GLU A:189 , LYS A:192
binding site for residue EDO A 506
07
AC7
SOFTWARE
ASN A:294 , LYS A:296
binding site for residue EDO A 507
08
AC8
SOFTWARE
ARG A:254 , HIS A:290
binding site for residue EDO A 508
09
AC9
SOFTWARE
ASP A:304 , SER A:349 , VAL A:352 , ASN A:356 , ARG A:400
binding site for residue EDO A 509
10
AD1
SOFTWARE
ARG A:365 , TYR A:368
binding site for residue EDO A 510
11
AD2
SOFTWARE
HOH A:607
binding site for residue EDO A 511
12
AD3
SOFTWARE
LYS A:120 , ASN A:159
binding site for residue EDO A 512
13
AD4
SOFTWARE
TYR B:118 , ASP B:263 , VAL B:264 , ASN B:265
binding site for residue SO4 B 401
14
AD5
SOFTWARE
PRO B:158 , ASP B:159 , VAL B:160 , LYS B:184
binding site for residue GOL B 402
15
AD6
SOFTWARE
ASN B:275 , ARG B:285 , PHE B:287 , GLU B:326
binding site for residue GOL B 403
16
AD7
SOFTWARE
ASP B:81 , ASN B:84 , TYR B:157 , LYS B:182 , HIS B:186
binding site for residue GOL B 404
17
AD8
SOFTWARE
THR B:156
binding site for residue EDO B 405
18
AD9
SOFTWARE
HIS B:39 , TYR B:40 , TYR B:147 , ASP B:148
binding site for residue EDO B 406
19
AE1
SOFTWARE
ARG B:69 , GLU B:94
binding site for residue EDO B 407
20
AE2
SOFTWARE
LYS B:213 , GLU B:215 , GLU B:226 , GLU B:228
binding site for residue EDO B 408
21
AE3
SOFTWARE
GLU B:77 , LEU B:78 , PHE B:79 , ASN B:80 , ALA B:124 , ASN B:125 , VAL B:126 , ARG B:127
binding site for residue EDO B 409
22
AE4
SOFTWARE
ILE B:216 , GLY B:218 , ASP B:263 , SER B:269
binding site for residue EDO B 410
23
AE5
SOFTWARE
GLU B:119 , GLN B:153 , PRO B:259 , ARG B:296
binding site for residue EDO B 411
24
AE6
SOFTWARE
LYS B:82 , ASN B:162 , SER B:163 , EDO B:414
binding site for residue EDO B 412
25
AE7
SOFTWARE
ARG B:139
binding site for residue EDO B 413
26
AE8
SOFTWARE
ASN B:80 , ASN B:161 , ASN B:162 , EDO B:412
binding site for residue EDO B 414
27
AE9
SOFTWARE
LYS B:214 , THR B:225
binding site for residue EDO B 415
28
AF1
SOFTWARE
ASP A:128 , LYS A:131 , THR C:8 , ARG C:10
binding site for residue EDO C 201
29
AF2
SOFTWARE
ARG C:70 , TYR C:71 , SER C:72 , SO4 C:203 , HOH C:308
binding site for residue SO4 C 202
30
AF3
SOFTWARE
LYS C:95 , ALA C:96 , GLN C:100 , ILE C:109 , ARG C:118 , SO4 C:202
binding site for residue SO4 C 203
31
AF4
SOFTWARE
SER C:34 , ASN C:35 , LYS C:119
binding site for residue SO4 C 204
32
AF5
SOFTWARE
LEU B:199 , ARG B:201 , LYS B:242 , SER C:26
binding site for residue GOL C 205
33
AF6
SOFTWARE
THR C:48 , ARG C:68 , ASP C:73 , ILE C:149
binding site for residue EDO C 206
34
AF7
SOFTWARE
ARG A:204 , ARG C:52
binding site for residue EDO C 207
35
AF8
SOFTWARE
LYS C:63
binding site for residue EDO C 208
[
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 B
Chain C
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 (165 KB)
Header - Asym.Unit
Biol.Unit 1 (158 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
5F0J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
