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.
3NQI
Asym. Unit
Info
Asym.Unit (329 KB)
Biol.Unit 1 (83 KB)
Biol.Unit 2 (85 KB)
Biol.Unit 3 (83 KB)
Biol.Unit 4 (82 KB)
Biol.Unit 5 (319 KB)
Biol.Unit 6 (315 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 A PUTATIVE LIPOPROTEIN (BF3042) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.87 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
29 Jun 10 (Deposition) - 18 Aug 10 (Release) - 18 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.87
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: A,B (2x)
Biol. Unit 6: C,D (2x)
Keywords
:
Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Lipid Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Lipoprotein (Bf3042) From Bacteroides Fragilis Nctc 9343 At 1. 87 A Resolution
To Be Published
[
close entry info
]
Hetero Components
(5, 52)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
2c: CADMIUM ION (CDc)
2d: CADMIUM ION (CDd)
2e: CADMIUM ION (CDe)
2f: CADMIUM ION (CDf)
2g: CADMIUM ION (CDg)
2h: CADMIUM ION (CDh)
2i: CADMIUM ION (CDi)
2j: CADMIUM ION (CDj)
2k: CADMIUM ION (CDk)
2l: CADMIUM ION (CDl)
2m: CADMIUM ION (CDm)
2n: CADMIUM ION (CDn)
2o: CADMIUM ION (CDo)
2p: CADMIUM ION (CDp)
2q: CADMIUM ION (CDq)
2r: CADMIUM ION (CDr)
2s: CADMIUM ION (CDs)
2t: CADMIUM ION (CDt)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
3h: CHLORIDE ION (CLh)
3i: CHLORIDE ION (CLi)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
5b: DI(HYDROXYETHYL)ETHER (PEGb)
5c: DI(HYDROXYETHYL)ETHER (PEGc)
5d: DI(HYDROXYETHYL)ETHER (PEGd)
5e: DI(HYDROXYETHYL)ETHER (PEGe)
5f: DI(HYDROXYETHYL)ETHER (PEGf)
5g: DI(HYDROXYETHYL)ETHER (PEGg)
5h: DI(HYDROXYETHYL)ETHER (PEGh)
5i: DI(HYDROXYETHYL)ETHER (PEGi)
5j: DI(HYDROXYETHYL)ETHER (PEGj)
5k: DI(HYDROXYETHYL)ETHER (PEGk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
CD
20
Ligand/Ion
CADMIUM ION
3
CL
9
Ligand/Ion
CHLORIDE ION
4
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
5
PEG
11
Ligand/Ion
DI(HYDROXYETHYL)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: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:184 , ILE A:186 , HOH A:384 , HOH A:530 , HOH A:678
BINDING SITE FOR RESIDUE CD A 300
02
AC2
SOFTWARE
ASP A:97 , CL A:328 , HOH A:347 , HOH A:354 , HOH A:356 , HOH A:496
BINDING SITE FOR RESIDUE CD A 301
03
AC3
SOFTWARE
GLU A:160 , GLU A:196 , CL A:323 , MSE B:43
BINDING SITE FOR RESIDUE CD A 302
04
AC4
SOFTWARE
GLU A:142 , GLU A:267 , HOH A:489 , GLU B:223 , HOH B:705
BINDING SITE FOR RESIDUE CD A 307
05
AC5
SOFTWARE
ILE A:186 , LYS A:235 , ILE B:186 , LYS B:235
BINDING SITE FOR RESIDUE CL A 321
06
AC6
SOFTWARE
GLU A:160 , GLU A:196 , CD A:302 , MSE B:43
BINDING SITE FOR RESIDUE CL A 323
07
AC7
SOFTWARE
VAL A:64 , THR A:65 , LEU A:66 , ASP A:97 , CD A:301
BINDING SITE FOR RESIDUE CL A 328
08
AC8
SOFTWARE
TYR A:72 , ILE A:101 , SER A:210 , SER A:211 , PHE A:212
BINDING SITE FOR RESIDUE PEG A 329
09
AC9
SOFTWARE
ASP A:50 , ALA A:51 , PHE A:140 , SER A:141
BINDING SITE FOR RESIDUE PEG A 332
10
BC1
SOFTWARE
GLN A:139 , PHE A:140 , THR A:265 , ALA A:266
BINDING SITE FOR RESIDUE PEG A 333
11
BC2
SOFTWARE
GLN A:241 , LEU A:249 , GLU A:250 , HOH A:477 , HOH A:556 , HOH A:631
BINDING SITE FOR RESIDUE PEG A 337
12
BC3
SOFTWARE
GLU A:223 , GLU B:142 , GLU B:267 , HOH B:412
BINDING SITE FOR RESIDUE CD B 303
13
BC4
SOFTWARE
HOH A:520 , ASP B:184 , ILE B:186 , HOH B:397 , HOH B:674
BINDING SITE FOR RESIDUE CD B 304
14
BC5
SOFTWARE
ASP B:97 , CL B:325 , HOH B:350 , HOH B:357 , HOH B:362 , HOH B:448
BINDING SITE FOR RESIDUE CD B 305
15
BC6
SOFTWARE
MSE A:43 , GLU B:160 , GLU B:196 , ACT B:342
BINDING SITE FOR RESIDUE CD B 306
16
BC7
SOFTWARE
GLU B:262 , LYS C:235 , GLU C:260
BINDING SITE FOR RESIDUE CD B 308
17
BC8
SOFTWARE
GLU B:198 , HOH B:613 , GLU C:79
BINDING SITE FOR RESIDUE CD B 309
18
BC9
SOFTWARE
GLU B:113 , HOH B:627 , LYS D:110 , GLU D:113
BINDING SITE FOR RESIDUE CD B 318
19
CC1
SOFTWARE
GLU A:260 , HOH A:429 , GLU B:260 , HOH B:464
BINDING SITE FOR RESIDUE CD B 319
20
CC2
SOFTWARE
ASN A:60 , ASN B:60
BINDING SITE FOR RESIDUE CL B 320
21
CC3
SOFTWARE
SER B:141 , THR B:144 , HOH B:683
BINDING SITE FOR RESIDUE CL B 322
22
CC4
SOFTWARE
VAL B:64 , THR B:65 , LEU B:66 , ASP B:97 , CD B:305
BINDING SITE FOR RESIDUE CL B 325
23
CC5
SOFTWARE
GLN B:139 , PHE B:140 , LYS B:264
BINDING SITE FOR RESIDUE PEG B 330
24
CC6
SOFTWARE
THR B:49 , ASP B:50 , ALA B:51 , PHE B:140 , HOH B:683
BINDING SITE FOR RESIDUE PEG B 331
25
CC7
SOFTWARE
GLN B:241 , LEU B:249 , GLU B:250 , THR B:254
BINDING SITE FOR RESIDUE PEG B 335
26
CC8
SOFTWARE
LYS A:181 , LYS B:110 , VAL B:111 , ASP B:179 , TYR B:190 , ARG B:192
BINDING SITE FOR RESIDUE PEG B 336
27
CC9
SOFTWARE
SER B:211 , PHE B:212 , HOH B:696
BINDING SITE FOR RESIDUE ACT B 341
28
DC1
SOFTWARE
MSE A:43 , THR B:158 , THR B:159 , GLU B:160 , GLU B:196 , CD B:306
BINDING SITE FOR RESIDUE ACT B 342
29
DC2
SOFTWARE
ASP C:97 , CL C:326 , HOH C:359 , HOH C:392 , HOH C:408 , HOH C:541
BINDING SITE FOR RESIDUE CD C 310
30
DC3
SOFTWARE
GLU C:160 , GLU C:196 , ACT C:343 , MSE D:43
BINDING SITE FOR RESIDUE CD C 311
31
DC4
SOFTWARE
HOH B:707 , GLU C:262 , CL C:324
BINDING SITE FOR RESIDUE CD C 313
32
DC5
SOFTWARE
GLU C:142 , GLU C:267 , HOH C:355 , GLU D:223
BINDING SITE FOR RESIDUE CD C 316
33
DC6
SOFTWARE
LYS B:232 , THR B:265 , HOH B:707 , GLU C:262 , LYS C:264 , CD C:313
BINDING SITE FOR RESIDUE CL C 324
34
DC7
SOFTWARE
VAL C:64 , THR C:65 , LEU C:66 , ASP C:97 , PRO C:98 , CD C:310
BINDING SITE FOR RESIDUE CL C 326
35
DC8
SOFTWARE
ILE C:101 , SER C:210 , SER C:211 , PHE C:212
BINDING SITE FOR RESIDUE PEG C 334
36
DC9
SOFTWARE
GLN C:241 , GLU C:250 , THR C:254 , GLU C:256
BINDING SITE FOR RESIDUE PEG C 338
37
EC1
SOFTWARE
THR C:158 , THR C:159 , GLU C:160 , GLU C:196 , CD C:311 , HOH C:668 , MSE D:43
BINDING SITE FOR RESIDUE ACT C 343
38
EC2
SOFTWARE
GLU C:223 , GLU D:142 , GLU D:267 , ACT D:340
BINDING SITE FOR RESIDUE CD D 312
39
EC3
SOFTWARE
ASP D:97 , CL D:327 , HOH D:495 , HOH D:514 , HOH D:515
BINDING SITE FOR RESIDUE CD D 314
40
EC4
SOFTWARE
MSE C:43 , THR D:159 , GLU D:160 , GLU D:196
BINDING SITE FOR RESIDUE CD D 315
41
EC5
SOFTWARE
GLU A:79 , GLU D:198
BINDING SITE FOR RESIDUE CD D 317
42
EC6
SOFTWARE
VAL D:64 , THR D:65 , LEU D:66 , ASP D:97 , CD D:314
BINDING SITE FOR RESIDUE CL D 327
43
EC7
SOFTWARE
GLN D:241 , LEU D:249 , GLU D:250 , THR D:254
BINDING SITE FOR RESIDUE PEG D 339
44
EC8
SOFTWARE
GLU C:223 , GLU D:142 , ALA D:266 , GLU D:267 , CD D:312
BINDING SITE FOR RESIDUE ACT D 340
[
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
(1, 4)
Info
all PFAM domains
1a: PFAM_NigD_3nqiD01 (D:38-253)
1b: PFAM_NigD_3nqiD02 (D:38-253)
1c: PFAM_NigD_3nqiD03 (D:38-253)
1d: PFAM_NigD_3nqiD04 (D:38-253)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NigD]
(4)
Family
:
NigD
(4)
Bacteroides fragilis (strain ATCC 25285 / NCTC 9343)
(1)
1a
NigD-3nqiD01
D:38-253
1b
NigD-3nqiD02
D:38-253
1c
NigD-3nqiD03
D:38-253
1d
NigD-3nqiD04
D:38-253
[
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 (329 KB)
Header - Asym.Unit
Biol.Unit 1 (83 KB)
Header - Biol.Unit 1
Biol.Unit 2 (85 KB)
Header - Biol.Unit 2
Biol.Unit 3 (83 KB)
Header - Biol.Unit 3
Biol.Unit 4 (82 KB)
Header - Biol.Unit 4
Biol.Unit 5 (319 KB)
Header - Biol.Unit 5
Biol.Unit 6 (315 KB)
Header - Biol.Unit 6
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
3NQI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help