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.
5VB2
Asym. Unit
Info
Asym.Unit (551 KB)
Biol.Unit 1 (534 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 NAVAB VOLTAGE-GATED SODIUM CHANNEL IN A CLOSED CONFORMATION
Authors
:
M. J. Lenaeus, W. A. Catterall
Date
:
28 Mar 17 (Deposition) - 05 Apr 17 (Release) - 19 Apr 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Voltage-Gated Sodium Channel, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Lenaeus, T. M. Gamal El-Din, C. Ing, K. Ramanadane, R. Pomes, N. Zheng, W. A. Catterall
Structures Of Closed And Open States Of A Voltage-Gated Sodium Channel.
Proc. Natl. Acad. Sci. V. 114 E3051 2017 U. S. A.
[
close entry info
]
Hetero Components
(4, 26)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSa)
2b: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSb)
2c: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSc)
2d: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSd)
2e: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSe)
2f: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSf)
2g: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSg)
2h: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMO... (CPSh)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
4a: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4a)
4b: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4b)
4c: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4c)
4d: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4d)
4e: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4e)
4f: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4f)
4g: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4g)
4h: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4h)
4i: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4i)
4j: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4j)
4k: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4k)
4l: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4l)
4m: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4m)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
CPS
8
Ligand/Ion
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
3
PO4
4
Ligand/Ion
PHOSPHATE ION
4
PX4
13
Ligand/Ion
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:1129 , ILE A:1216 , ASP A:1219 , ILE A:1223 , HOH A:1405 , ILE D:2119
binding site for residue CPS A 1301
02
AC2
SOFTWARE
SER A:1125 , VAL A:1126 , ALA A:1220 , VAL B:2218 , ASP B:2219
binding site for residue CPS A 1302
03
AC3
SOFTWARE
MET A:1188 , PRO A:1192 , TRP A:1195 , HOH A:1401 , MET D:2137 , THR D:2162 , GLY D:2164 , GLU D:2165 , PHE D:2167 , TYR D:2168
binding site for residue PX4 A 1303
04
AC4
SOFTWARE
GLY A:1030 , SER A:1034 , THR B:2162 , GLY B:2164 , PX4 B:2306
binding site for residue PX4 A 1304
05
AC5
SOFTWARE
PHE A:1144 , ARG A:1155 , TYR A:1191 , TYR A:1193 , HOH A:1402 , ILE D:2097
binding site for residue PX4 A 1305
06
AC6
SOFTWARE
TRP A:1076 , SER A:1121
binding site for residue PO4 A 1306
07
AC7
SOFTWARE
ILE A:1119 , GLY B:2129 , ILE B:2216 , ASP B:2219 , ALA B:2220 , ILE B:2223 , HOH B:2404
binding site for residue CPS B 2301
08
AC8
SOFTWARE
ALA B:2122 , SER B:2125 , VAL B:2126 , ILE B:2223 , LEU B:2224
binding site for residue CPS B 2302
09
AC9
SOFTWARE
ILE A:1097 , LEU B:2151 , PHE B:2152 , ARG B:2155 , TYR B:2191 , VAL B:2196 , HOH B:2405
binding site for residue PX4 B 2303
10
AD1
SOFTWARE
MET A:1137 , PHE A:1141 , GLY A:1164 , PHE A:1167 , TYR A:1168 , MET B:2188 , PRO B:2192 , TRP B:2195 , PX4 D:2303
binding site for residue PX4 B 2304
11
AD2
SOFTWARE
GLY B:2030 , LEU B:2031 , SER B:2034 , THR B:2036 , TYR C:1142 , THR C:1162 , GLY C:1164
binding site for residue PX4 B 2305
12
AD3
SOFTWARE
PX4 A:1304 , MET B:2137 , PHE B:2141 , GLY B:2164 , GLU B:2165 , HOH B:2403 , MET C:1188 , PRO C:1192
binding site for residue PX4 B 2306
13
AD4
SOFTWARE
SER C:1125 , VAL C:1126 , ALA C:1220 , VAL D:2218 , ASP D:2219
binding site for residue CPS C 1301
14
AD5
SOFTWARE
ILE B:2119 , GLY C:1129 , ILE C:1216 , ASP C:1219
binding site for residue CPS C 1302
15
AD6
SOFTWARE
GLY C:1030 , LEU C:1031 , SER C:1034 , THR D:2162 , LEU D:2163
binding site for residue PX4 C 1303
16
AD7
SOFTWARE
GLY C:1164 , GLU C:1165 , PHE C:1167 , TYR C:1168 , MET D:2188 , TRP D:2195
binding site for residue PX4 C 1304
17
AD8
SOFTWARE
ILE B:2097 , PHE C:1144 , LEU C:1151 , PHE C:1152 , VAL C:1190 , TYR C:1191 , TYR C:1193 , HOH C:1404
binding site for residue PX4 C 1305
18
AD9
SOFTWARE
SER C:1121
binding site for residue PO4 C 1306
19
AE1
SOFTWARE
HIS A:1239 , HIS B:2239 , HIS C:1239 , HIS D:2239
binding site for residue CL C 1307
20
AE2
SOFTWARE
ILE C:1119 , GLY D:2129 , ASP D:2219 , ALA D:2220 , ILE D:2223
binding site for residue CPS D 2301
21
AE3
SOFTWARE
ASP A:1219 , ALA D:2122 , SER D:2125 , VAL D:2126 , ILE D:2223
binding site for residue CPS D 2302
22
AE4
SOFTWARE
THR A:1162 , GLY A:1164 , PX4 B:2304 , GLY D:2030 , LEU D:2031 , SER D:2034
binding site for residue PX4 D 2303
23
AE5
SOFTWARE
ILE C:1097 , LEU D:2151 , TYR D:2191 , TYR D:2193 , VAL D:2196
binding site for residue PX4 D 2304
24
AE6
SOFTWARE
PRO D:2075 , TRP D:2076 , PHE D:2079 , SER D:2121 , ILE D:2124
binding site for residue PX4 D 2305
25
AE7
SOFTWARE
GLN C:1115 , SER D:2132
binding site for residue PO4 D 2306
[
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
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 (551 KB)
Header - Asym.Unit
Biol.Unit 1 (534 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
5VB2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
