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.
4MLB
Biol. Unit 1
Info
Asym.Unit (311 KB)
Biol.Unit 1 (156 KB)
Biol.Unit 2 (77 KB)
Biol.Unit 3 (81 KB)
Biol.Unit 4 (76 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
REVERSE POLARITY OF BINDING POCKET SUGGESTS DIFFERENT FUNCTION OF A MOP SUPERFAMILY TRANSPORTER FROM PYROCOCCUS FURIOSUS VC1 (DSM3638)
Authors
:
V. N. Malviya, T. Nonaka, C. Muenke, J. Koepke, H. Michel
Date
:
06 Sep 13 (Deposition) - 25 Sep 13 (Release) - 22 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Lipid Translocase, Flippase, Membrane Protein, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. N. Malviya, T. Nonaka, C. Muenke, J. Koepke, H. Michel
Reverse Polarity Of Binding Pocket Suggests Different Function Of A Mop Superfamily Transporter From Pyrococcus Furiosus Vc1 (Dsm3638)
To Be Published
[
close entry info
]
Hetero Components
(1, 33)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEa)
2aa: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEaa)
2ab: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEab)
2ac: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEac)
2ad: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEad)
2ae: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEae)
2af: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEaf)
2ag: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEag)
2ah: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEah)
2ai: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEai)
2aj: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEaj)
2ak: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEak)
2al: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEal)
2am: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEam)
2an: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEan)
2ao: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEao)
2ap: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEap)
2aq: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEaq)
2ar: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEar)
2as: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEas)
2at: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEat)
2au: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEau)
2av: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEav)
2aw: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEaw)
2ax: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEax)
2ay: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEay)
2az: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEaz)
2b: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEb)
2ba: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEba)
2c: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEc)
2d: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEd)
2e: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEe)
2f: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEf)
2g: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEg)
2h: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEh)
2i: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEi)
2j: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEj)
2k: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEk)
2l: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEl)
2m: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEm)
2n: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEn)
2o: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEo)
2p: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEp)
2q: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEq)
2r: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEr)
2s: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEs)
2t: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEt)
2u: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEu)
2v: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEv)
2w: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEw)
2x: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEx)
2y: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEy)
2z: PENTAETHYLENE GLYCOL MONODECYL ETH... (CXEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
CXE
33
Ligand/Ion
PENTAETHYLENE GLYCOL MONODECYL ETHER
[
close Hetero Component info
]
Sites
(44, 44)
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)
22: CC6 (SOFTWARE)
23: DC1 (SOFTWARE)
24: DC3 (SOFTWARE)
25: DC4 (SOFTWARE)
26: DC5 (SOFTWARE)
27: DC6 (SOFTWARE)
28: DC7 (SOFTWARE)
29: DC8 (SOFTWARE)
30: DC9 (SOFTWARE)
31: EC1 (SOFTWARE)
32: EC2 (SOFTWARE)
33: EC3 (SOFTWARE)
34: EC4 (SOFTWARE)
35: EC5 (SOFTWARE)
36: EC6 (SOFTWARE)
37: EC7 (SOFTWARE)
38: EC8 (SOFTWARE)
39: EC9 (SOFTWARE)
40: FC1 (SOFTWARE)
41: FC3 (SOFTWARE)
42: FC4 (SOFTWARE)
43: FC5 (SOFTWARE)
44: FC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:7 , ASP A:165 , ASN A:167 , CXE A:506 , CXE A:515 , HOH A:651 , TRP B:44
BINDING SITE FOR RESIDUE CXE A 501
02
AC2
SOFTWARE
ILE A:181 , PRO A:185 , TYR A:189 , THR A:190 , LEU B:171 , VAL B:174 , CXE B:503
BINDING SITE FOR RESIDUE CXE A 502
03
AC3
SOFTWARE
TYR A:322 , CXE A:509 , CXE B:506
BINDING SITE FOR RESIDUE CXE A 503
04
AC4
SOFTWARE
LEU A:101 , PHE A:218 , ILE A:227 , LEU A:229 , CXE A:517 , HOH A:665 , THR D:190 , LEU D:191
BINDING SITE FOR RESIDUE CXE A 504
05
AC5
SOFTWARE
TYR A:347 , CXE B:511
BINDING SITE FOR RESIDUE CXE A 505
06
AC6
SOFTWARE
LEU A:171 , VAL A:174 , LEU A:175 , TRP A:216 , CXE A:501 , ILE B:181 , PRO B:185 , TYR B:189 , THR B:190
BINDING SITE FOR RESIDUE CXE A 506
07
AC7
SOFTWARE
PHE A:378
BINDING SITE FOR RESIDUE CXE A 507
08
AC8
SOFTWARE
PHE A:341 , GLN A:344 , LYS D:453
BINDING SITE FOR RESIDUE CXE A 508
09
AC9
SOFTWARE
SER A:32 , LEU A:288 , CXE A:503 , LEU B:36
BINDING SITE FOR RESIDUE CXE A 509
10
BC1
SOFTWARE
LEU A:69
BINDING SITE FOR RESIDUE CXE A 510
11
BC2
SOFTWARE
ALA A:145 , PHE A:148 , CXE C:513
BINDING SITE FOR RESIDUE CXE A 511
12
BC3
SOFTWARE
SER A:210
BINDING SITE FOR RESIDUE CXE A 512
13
BC4
SOFTWARE
MET A:64 , LEU A:69 , SER A:250 , SER A:257
BINDING SITE FOR RESIDUE CXE A 513
14
BC5
SOFTWARE
CXE A:501
BINDING SITE FOR RESIDUE CXE A 515
15
BC6
SOFTWARE
PHE A:218 , CXE A:517 , MET C:329 , CXE C:514 , THR D:190
BINDING SITE FOR RESIDUE CXE A 516
16
BC7
SOFTWARE
CXE A:504 , CXE A:516 , CXE C:505
BINDING SITE FOR RESIDUE CXE A 517
17
BC8
SOFTWARE
TRP A:216 , HOH A:652 , HOH A:671 , THR B:190
BINDING SITE FOR RESIDUE CL A 518
18
BC9
SOFTWARE
THR A:190 , TRP B:216
BINDING SITE FOR RESIDUE CL A 519
19
CC1
SOFTWARE
THR A:190 , LEU A:191 , TYR B:215 , LEU C:39 , ILE C:43 , LYS D:4
BINDING SITE FOR RESIDUE CXE B 501
20
CC2
SOFTWARE
THR B:190 , LEU B:191 , GLY B:192 , VAL C:21 , CXE C:505
BINDING SITE FOR RESIDUE CXE B 502
21
CC3
SOFTWARE
TRP A:44 , CXE A:502 , LYS B:7 , GLY B:8 , LEU B:11 , ASP B:165 , ASN B:167 , ARG B:168 , CXE B:509
BINDING SITE FOR RESIDUE CXE B 503
22
CC6
SOFTWARE
CXE A:503 , PHE B:337 , GLN B:344
BINDING SITE FOR RESIDUE CXE B 506
23
DC1
SOFTWARE
CXE A:505 , ILE B:25
BINDING SITE FOR RESIDUE CXE B 511
24
DC3
SOFTWARE
VAL B:109 , ILE B:113 , VAL C:208 , PHE C:212 , TYR C:215 , VAL C:219 , CXE C:503
BINDING SITE FOR RESIDUE CXE C 501
25
DC4
SOFTWARE
LEU A:442 , HOH A:633 , LEU C:229 , ARG C:230 , ASP C:231
BINDING SITE FOR RESIDUE CXE C 502
26
DC5
SOFTWARE
ILE B:113 , SER C:210 , LEU C:211 , ALA C:214 , CXE C:501
BINDING SITE FOR RESIDUE CXE C 503
27
DC6
SOFTWARE
GLU C:391 , LYS C:394 , ARG C:447 , CXE C:515 , HOH C:613 , CXE D:501
BINDING SITE FOR RESIDUE CXE C 504
28
DC7
SOFTWARE
CXE A:517 , CXE B:502 , TYR C:322 , ILE C:326 , MET C:329 , CXE C:514 , HOH C:699
BINDING SITE FOR RESIDUE CXE C 505
29
DC8
SOFTWARE
LEU C:101 , ARG C:221 , ILE C:227 , THR C:228 , LEU C:229 , CXE C:516
BINDING SITE FOR RESIDUE CXE C 506
30
DC9
SOFTWARE
LEU C:404 , CXE D:504
BINDING SITE FOR RESIDUE CXE C 507
31
EC1
SOFTWARE
PHE C:410 , CXE D:505
BINDING SITE FOR RESIDUE CXE C 508
32
EC2
SOFTWARE
GLY C:192 , PHE C:193
BINDING SITE FOR RESIDUE CXE C 509
33
EC3
SOFTWARE
TYR A:417 , ALA C:145
BINDING SITE FOR RESIDUE CXE C 510
34
EC4
SOFTWARE
PRO C:61 , GLY C:65 , LEU C:69 , LEU C:247 , SER C:250 , LEU C:254 , SER C:257
BINDING SITE FOR RESIDUE CXE C 511
35
EC5
SOFTWARE
TYR C:37 , ASN C:38 , PHE C:63 , ALA C:172 , GLY C:176 , ASN C:180 , THR C:202 , THR C:209
BINDING SITE FOR RESIDUE CXE C 512
36
EC6
SOFTWARE
ARG A:141 , VAL A:142 , ALA A:145 , PHE A:193 , TYR A:200 , CXE A:511 , LEU C:340 , PHE C:341 , PRO C:343 , GLN C:344 , TYR C:347 , LEU C:348 , LYS C:359
BINDING SITE FOR RESIDUE CXE C 513
37
EC7
SOFTWARE
CXE A:516 , LEU C:321 , LYS C:325 , CXE C:505 , TYR D:189
BINDING SITE FOR RESIDUE CXE C 514
38
EC8
SOFTWARE
CXE C:504
BINDING SITE FOR RESIDUE CXE C 515
39
EC9
SOFTWARE
PHE C:218 , CXE C:506
BINDING SITE FOR RESIDUE CXE C 516
40
FC1
SOFTWARE
VAL C:439 , TRP C:443 , CXE C:504 , TYR D:347
BINDING SITE FOR RESIDUE CXE D 501
41
FC3
SOFTWARE
TYR C:417 , ILE D:25 , MET D:28 , SER D:32 , CXE D:505
BINDING SITE FOR RESIDUE CXE D 503
42
FC4
SOFTWARE
CXE C:507 , PHE D:337
BINDING SITE FOR RESIDUE CXE D 504
43
FC5
SOFTWARE
CXE C:508 , MET D:329 , CXE D:503
BINDING SITE FOR RESIDUE CXE D 505
44
FC7
SOFTWARE
PHE C:441 , TRP D:44 , TYR D:189
BINDING SITE FOR RESIDUE CXE D 507
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
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 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 (311 KB)
Header - Asym.Unit
Biol.Unit 1 (156 KB)
Header - Biol.Unit 1
Biol.Unit 2 (77 KB)
Header - Biol.Unit 2
Biol.Unit 3 (81 KB)
Header - Biol.Unit 3
Biol.Unit 4 (76 KB)
Header - Biol.Unit 4
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
4MLB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
