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.
3PND
Biol. Unit 2
Info
Asym.Unit (428 KB)
Biol.Unit 1 (210 KB)
Biol.Unit 2 (212 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FAD BINDING BY APBE PROTEIN FROM SALMONELLA ENTERICA: A NEW CLASS OF FAD BINDING PROTEINS
Authors
:
J. M. Boyd, J. A. Endrizzi, T. L. Hamilton, M. R. Christopherson, D. W. Mu D. M. Downs, J. W. Peters
Date
:
18 Nov 10 (Deposition) - 05 Jan 11 (Release) - 02 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Apbe, Fad, Flavoprotein, Oxidoreductase, Fad Binding Domain, T-Fold, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Boyd, J. A. Endrizzi, T. L. Hamilton, M. R. Christopherson, D. W. Mulder, D. M. Downs, J. W. Peters
Fad Binding By Apbe Protein From Salmonella Enterica: A New Class Of Fad-Binding Proteins.
J. Bacteriol. V. 193 887 2011
[
close entry info
]
Hetero Components
(2, 21)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2a: SULFATE ION (SO4a)
2aa: SULFATE ION (SO4aa)
2ab: SULFATE ION (SO4ab)
2ac: SULFATE ION (SO4ac)
2ad: SULFATE ION (SO4ad)
2ae: SULFATE ION (SO4ae)
2af: SULFATE ION (SO4af)
2ag: SULFATE ION (SO4ag)
2ah: SULFATE ION (SO4ah)
2ai: SULFATE ION (SO4ai)
2aj: SULFATE ION (SO4aj)
2ak: SULFATE ION (SO4ak)
2al: SULFATE ION (SO4al)
2am: SULFATE ION (SO4am)
2an: SULFATE ION (SO4an)
2ao: SULFATE ION (SO4ao)
2ap: SULFATE ION (SO4ap)
2aq: SULFATE ION (SO4aq)
2ar: SULFATE ION (SO4ar)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
2x: SULFATE ION (SO4x)
2y: SULFATE ION (SO4y)
2z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
SO4
19
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC7 (SOFTWARE)
08: CC2 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC7 (SOFTWARE)
11: DC1 (SOFTWARE)
12: DC2 (SOFTWARE)
13: DC3 (SOFTWARE)
14: DC4 (SOFTWARE)
15: DC5 (SOFTWARE)
16: DC6 (SOFTWARE)
17: DC7 (SOFTWARE)
18: DC8 (SOFTWARE)
19: DC9 (SOFTWARE)
20: EC1 (SOFTWARE)
21: EC2 (SOFTWARE)
22: EC3 (SOFTWARE)
23: EC4 (SOFTWARE)
24: EC5 (SOFTWARE)
25: EC6 (SOFTWARE)
26: EC7 (SOFTWARE)
27: EC8 (SOFTWARE)
28: EC9 (SOFTWARE)
29: FC1 (SOFTWARE)
30: FC2 (SOFTWARE)
31: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
GLY A:255 , SER A:256 , ASN A:259 , SO4 A:364 , GLU C:37
BINDING SITE FOR RESIDUE SO4 A 358
02
AC5
SOFTWARE
ASN A:283 , LYS A:328 , GLY A:330 , ARG C:91
BINDING SITE FOR RESIDUE SO4 A 361
03
AC6
SOFTWARE
ARG A:267 , HIS A:270 , LYS C:39
BINDING SITE FOR RESIDUE SO4 A 362
04
AC8
SOFTWARE
MET A:41 , THR A:43 , ASP A:72 , SER A:76 , TYR A:78 , ALA A:119 , MET A:120 , ASP A:121 , VAL A:124 , ASP A:181 , SER A:183 , THR A:184 , GLU A:187 , ARG A:267 , HIS A:270 , VAL A:271 , ILE A:272 , SO4 A:364 , HOH A:402 , HOH A:562 , LYS C:39
BINDING SITE FOR RESIDUE FAD A 500
05
BC1
SOFTWARE
ARG A:317 , TRP A:336 , HOH A:411 , GLN C:147
BINDING SITE FOR RESIDUE SO4 A 365
06
BC2
SOFTWARE
GLN A:310 , GLU A:329 , LYS A:334 , ARG C:91 , ASP C:177
BINDING SITE FOR RESIDUE SO4 A 366
07
BC7
SOFTWARE
HIS B:89 , ARG D:318
BINDING SITE FOR RESIDUE SO4 B 358
08
CC2
SOFTWARE
ARG B:91 , PRO B:176 , ASP B:177 , HOH B:523 , HOH B:528 , ARG D:318 , GLU D:319
BINDING SITE FOR RESIDUE SO4 B 362
09
CC5
SOFTWARE
SER B:256 , ARG B:258 , HOH B:408 , ARG D:258
BINDING SITE FOR RESIDUE SO4 B 365
10
CC7
SOFTWARE
HOH B:2 , HOH B:4 , MET B:41 , THR B:43 , ASP B:72 , SER B:76 , TYR B:78 , ALA B:119 , ASP B:121 , VAL B:124 , PHE B:133 , ASP B:181 , SER B:183 , THR B:184 , GLU B:187 , HIS B:270 , ILE B:272 , HOH B:439 , HOH B:557 , LYS D:39
BINDING SITE FOR RESIDUE FAD B 500
11
DC1
SOFTWARE
HOH A:6 , ASP A:174 , HOH A:399 , ASN C:80 , ASP C:81
BINDING SITE FOR RESIDUE SO4 C 357
12
DC2
SOFTWARE
ARG B:91 , PRO B:176 , HOH B:409 , SER C:99 , GLU C:100 , HOH C:409
BINDING SITE FOR RESIDUE SO4 C 358
13
DC3
SOFTWARE
TYR C:189 , ASP C:192 , ARG C:196 , LEU C:295 , HOH C:414
BINDING SITE FOR RESIDUE SO4 C 359
14
DC4
SOFTWARE
LYS A:39 , HOH A:426 , PHE C:133 , HIS C:270
BINDING SITE FOR RESIDUE SO4 C 360
15
DC5
SOFTWARE
GLY C:218 , ASN C:247 , HOH C:400 , GLY D:218 , ASN D:247
BINDING SITE FOR RESIDUE SO4 C 361
16
DC6
SOFTWARE
GLU A:37 , SER C:256 , SO4 C:367 , HOH C:418
BINDING SITE FOR RESIDUE SO4 C 362
17
DC7
SOFTWARE
HIS C:282 , ASN C:283 , LEU C:284 , GLY C:308 , THR C:309
BINDING SITE FOR RESIDUE SO4 C 363
18
DC8
SOFTWARE
PRO C:126 , ASN C:129 , TYR C:179 , HOH C:377
BINDING SITE FOR RESIDUE SO4 C 364
19
DC9
SOFTWARE
LYS A:39 , HOH C:15 , MET C:41 , THR C:43 , ASP C:72 , SER C:76 , TYR C:78 , ALA C:119 , MET C:120 , ASP C:121 , VAL C:124 , ASP C:181 , SER C:183 , THR C:184 , GLU C:187 , ARG C:267 , HIS C:270 , VAL C:271 , ILE C:272 , SO4 C:367 , HOH C:373 , HOH C:374 , HOH C:390 , HOH C:498
BINDING SITE FOR RESIDUE FAD C 500
20
EC1
SOFTWARE
THR C:26 , THR C:27 , THR C:28 , GLN D:172
BINDING SITE FOR RESIDUE SO4 C 365
21
EC2
SOFTWARE
GLN A:224 , ARG A:227 , ARG C:236 , HOH C:559
BINDING SITE FOR RESIDUE SO4 C 366
22
EC3
SOFTWARE
ARG C:267 , SER C:269 , HIS C:270 , VAL C:271 , SO4 C:362 , HOH C:392 , FAD C:500
BINDING SITE FOR RESIDUE SO4 C 367
23
EC4
SOFTWARE
SER D:99 , GLU D:100 , GLN D:169
BINDING SITE FOR RESIDUE SO4 D 357
24
EC5
SOFTWARE
ARG D:165 , ALA D:166 , HIS D:168
BINDING SITE FOR RESIDUE SO4 D 358
25
EC6
SOFTWARE
GLU B:37 , GLY D:255 , ARG D:267 , HOH D:381 , HOH D:388 , HOH D:429
BINDING SITE FOR RESIDUE SO4 D 359
26
EC7
SOFTWARE
HIS D:282 , ASN D:283 , LEU D:284 , GLY D:308 , THR D:309
BINDING SITE FOR RESIDUE SO4 D 360
27
EC8
SOFTWARE
ARG B:258 , GLN D:231 , SER D:256 , TYR D:257 , ARG D:258
BINDING SITE FOR RESIDUE SO4 D 361
28
EC9
SOFTWARE
LYS B:39 , MET D:41 , GLY D:42 , THR D:43 , ASP D:72 , SER D:76 , TYR D:78 , ALA D:119 , MET D:120 , ASP D:121 , VAL D:124 , VAL D:128 , PHE D:133 , ASP D:181 , SER D:183 , THR D:184 , GLU D:187 , ARG D:267 , HIS D:270 , VAL D:271 , ILE D:272 , HOH D:368 , HOH D:396 , HOH D:401 , HOH D:513
BINDING SITE FOR RESIDUE FAD D 500
29
FC1
SOFTWARE
GLY B:330 , GLU B:331 , SER D:90 , ARG D:91 , SER D:92
BINDING SITE FOR RESIDUE SO4 D 362
30
FC2
SOFTWARE
GLN D:158 , HIS D:159
BINDING SITE FOR RESIDUE SO4 D 363
31
FC3
SOFTWARE
TYR B:261 , GLN D:224 , ARG D:227
BINDING SITE FOR RESIDUE SO4 D 364
[
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
(1, 4)
Info
all PFAM domains
1a: PFAM_ApbE_3pndD01 (D:68-326)
1b: PFAM_ApbE_3pndD02 (D:68-326)
1c: PFAM_ApbE_3pndD03 (D:68-326)
1d: PFAM_ApbE_3pndD04 (D:68-326)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: ApbE]
(4)
Family
:
ApbE
(4)
Salmonella typhimurium
(1)
1a
ApbE-3pndD01
D:68-326
1b
ApbE-3pndD02
D:68-326
1c
ApbE-3pndD03
D:68-326
1d
ApbE-3pndD04
D:68-326
[
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 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 (428 KB)
Header - Asym.Unit
Biol.Unit 1 (210 KB)
Header - Biol.Unit 1
Biol.Unit 2 (212 KB)
Header - Biol.Unit 2
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
3PND
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help