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.
5ELF
Asym. Unit
Info
Asym.Unit (218 KB)
Biol.Unit 1 (106 KB)
Biol.Unit 2 (107 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CHOLERA TOXIN EL TOR B-PENTAMER IN COMPLEX WITH A-PENTASACCHARIDE
Authors
:
J. E. Heggelund, D. Burschowsky, U. Krengel
Date
:
04 Nov 15 (Deposition) - 30 Mar 16 (Release) - 27 Apr 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Keywords
:
Cholera Toxin B-Pentamer, Human Milk Oligosaccharide, Complex, Blood Group Oligosaccharide/Antigen, Toxin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. E. Heggelund, D. Burschowsky, V. A. Bjrnestad, V. Hodnik, G. Anderluh, U. Krengel
High-Resolution Crystal Structures Elucidate The Molecular Basis Of Cholera Blood Group Dependence.
Plos Pathog. V. 12 05567 2016
[
close entry info
]
Hetero Components
(8, 60)
Info
All Hetero Components
1a: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ga)
1b: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gb)
1c: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gc)
1d: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gd)
1e: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ge)
1f: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gf)
1g: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gg)
2a: BICINE (BCNa)
2b: BICINE (BCNb)
2c: BICINE (BCNc)
2d: BICINE (BCNd)
2e: BICINE (BCNe)
2f: BICINE (BCNf)
2g: BICINE (BCNg)
2h: BICINE (BCNh)
2i: BICINE (BCNi)
2j: BICINE (BCNj)
3a: BETA-D-GLUCOSE (BGCa)
3b: BETA-D-GLUCOSE (BGCb)
3c: BETA-D-GLUCOSE (BGCc)
4a: CALCIUM ION (CAa)
4b: CALCIUM ION (CAb)
4c: CALCIUM ION (CAc)
4d: CALCIUM ION (CAd)
4e: CALCIUM ION (CAe)
4f: CALCIUM ION (CAf)
4g: CALCIUM ION (CAg)
4h: CALCIUM ION (CAh)
4i: CALCIUM ION (CAi)
4j: CALCIUM ION (CAj)
5a: ALPHA-L-FUCOSE (FUCa)
5b: ALPHA-L-FUCOSE (FUCb)
5c: ALPHA-L-FUCOSE (FUCc)
5d: ALPHA-L-FUCOSE (FUCd)
5e: ALPHA-L-FUCOSE (FUCe)
5f: ALPHA-L-FUCOSE (FUCf)
5g: ALPHA-L-FUCOSE (FUCg)
5h: ALPHA-L-FUCOSE (FUCh)
5i: ALPHA-L-FUCOSE (FUCi)
5j: ALPHA-L-FUCOSE (FUCj)
5k: ALPHA-L-FUCOSE (FUCk)
5l: ALPHA-L-FUCOSE (FUCl)
5m: ALPHA-L-FUCOSE (FUCm)
5n: ALPHA-L-FUCOSE (FUCn)
5o: ALPHA-L-FUCOSE (FUCo)
5p: ALPHA-L-FUCOSE (FUCp)
6a: BETA-D-GALACTOSE (GALa)
6b: BETA-D-GALACTOSE (GALb)
6c: BETA-D-GALACTOSE (GALc)
6d: BETA-D-GALACTOSE (GALd)
6e: BETA-D-GALACTOSE (GALe)
6f: BETA-D-GALACTOSE (GALf)
6g: BETA-D-GALACTOSE (GALg)
7a: ALPHA-D-GLUCOSE (GLCa)
7b: ALPHA-D-GLUCOSE (GLCb)
7c: ALPHA-D-GLUCOSE (GLCc)
7d: ALPHA-D-GLUCOSE (GLCd)
7e: ALPHA-D-GLUCOSE (GLCe)
7f: ALPHA-D-GLUCOSE (GLCf)
8a: TETRAETHYLENE GLYCOL (PG4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A2G
7
Ligand/Ion
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2
BCN
10
Ligand/Ion
BICINE
3
BGC
3
Ligand/Ion
BETA-D-GLUCOSE
4
CA
10
Ligand/Ion
CALCIUM ION
5
FUC
16
Ligand/Ion
ALPHA-L-FUCOSE
6
GAL
7
Ligand/Ion
BETA-D-GALACTOSE
7
GLC
6
Ligand/Ion
ALPHA-D-GLUCOSE
8
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:79 , BCN A:202 , GLU F:79 , ASN J:103
binding site for residue CA A 201
02
AC2
SOFTWARE
GLU A:79 , CA A:201 , HOH A:321 , HOH A:342 , TYR F:76 , LEU F:77 , GLU F:79 , HOH F:324 , ALA J:80 , LYS J:81 , ASN J:103
binding site for residue BCN A 202
03
AC3
SOFTWARE
GLU A:79 , BCN A:204 , ASN E:103 , GLU F:79
binding site for residue CA A 203
04
AC4
SOFTWARE
TYR A:76 , LEU A:77 , GLU A:79 , CA A:203 , HOH A:311 , HOH A:321 , HOH A:329 , HOH A:363 , HOH A:367 , ALA E:80 , LYS E:81 , ASN E:103 , LYS F:23 , GLU F:79
binding site for residue BCN A 204
05
AC5
SOFTWARE
ALA A:80 , LYS A:81 , ASN A:103 , TYR B:76 , LEU B:77 , GLU B:79 , CA B:205 , HOH B:303 , HOH B:305 , HOH B:372 , GLU J:79 , HOH J:367
binding site for residue BCN B 201
06
AC6
SOFTWARE
GLU B:79 , BCN B:204 , HOH I:327 , GLU J:79
binding site for residue CA B 202
07
AC7
SOFTWARE
GLN A:3 , TYR B:18 , ILE B:47 , PHE B:48 , PRO B:93 , HIS B:94 , HOH B:308 , HOH B:352
binding site for residue FUC B 203
08
AC8
SOFTWARE
GLU B:79 , CA B:202 , HOH B:322 , HOH B:365 , HOH B:372 , ALA I:80 , LYS I:81 , ASN I:103 , HOH I:327 , TYR J:76 , LEU J:77 , GLU J:79 , HOH J:319
binding site for residue BCN B 204
09
AC9
SOFTWARE
GLU B:79 , BCN B:201 , GLU J:79 , HOH J:367
binding site for residue CA B 205
10
AD1
SOFTWARE
GLU C:79 , BCN C:203 , HOH C:345 , GLU I:79
binding site for residue CA C 201
11
AD2
SOFTWARE
ALA B:80 , LYS B:81 , ASN B:103 , HOH B:317 , HOH B:341 , LYS C:23 , TYR C:76 , LEU C:77 , GLU C:79 , CA C:204 , HOH C:301 , HOH C:304 , HOH C:311 , GLU I:79
binding site for residue BCN C 202
12
AD3
SOFTWARE
GLU C:79 , CA C:201 , HOH C:304 , HOH C:313 , HOH C:345 , ALA H:80 , LYS H:81 , ASN H:103 , TYR I:76 , LEU I:77 , GLU I:79 , HOH I:317
binding site for residue BCN C 203
13
AD4
SOFTWARE
HOH B:341 , GLU C:79 , BCN C:202 , GLU I:79
binding site for residue CA C 204
14
AD5
SOFTWARE
HOH C:370 , GLU D:79 , BCN D:203 , GLU H:79
binding site for residue CA D 201
15
AD6
SOFTWARE
ALA C:80 , LYS C:81 , ASN C:103 , HOH C:364 , TYR D:76 , LEU D:77 , GLU D:79 , CA D:204 , HOH D:317 , HOH D:341 , LYS H:23 , GLU H:79
binding site for residue BCN D 202
16
AD7
SOFTWARE
HOH C:370 , LYS D:23 , GLU D:79 , CA D:201 , ALA G:80 , LYS G:81 , ASN G:103 , TYR H:76 , LEU H:77 , GLU H:79 , HOH H:328
binding site for residue BCN D 203
17
AD8
SOFTWARE
ASN C:103 , GLU D:79 , BCN D:202 , GLU H:79
binding site for residue CA D 204
18
AD9
SOFTWARE
GLY D:45 , BGC D:205 , GAL D:206 , FUC D:208 , FUC D:209 , HOH D:305 , HOH D:323 , HOH D:350
binding site for residue GLC D 210
19
AE1
SOFTWARE
LYS D:81 , ASN D:103 , TYR E:76 , LEU E:77 , GLU E:79 , CA E:204 , HOH E:304 , HOH E:310 , LYS G:23 , GLU G:79 , HOH G:304
binding site for residue BCN E 201
20
AE2
SOFTWARE
GLU E:79 , BCN E:203 , HOH E:303 , GLU G:79
binding site for residue CA E 202
21
AE3
SOFTWARE
GLU E:79 , CA E:202 , HOH E:303 , ALA F:80 , LYS F:81 , ASN F:103 , TYR G:76 , LEU G:77 , GLU G:79 , HOH G:312 , HOH G:340
binding site for residue BCN E 203
22
AE4
SOFTWARE
GLU E:79 , BCN E:201 , GLU G:79 , HOH G:304
binding site for residue CA E 204
23
AE5
SOFTWARE
LYS F:34 , HOH F:367 , ALA H:10 , GLU H:11 , TYR H:12 , HIS H:13 , GLU J:11 , TYR J:12
binding site for residue PG4 F 201
24
AE6
SOFTWARE
GLY G:45 , GAL G:202 , FUC G:204 , FUC G:205 , GLC G:206 , HOH G:301 , HOH G:303 , HOH G:331 , HOH G:386 , HOH G:395 , ASN J:90
binding site for residue BGC G 201
25
AE7
SOFTWARE
GLN G:3 , ILE H:47 , PHE H:48 , PRO H:93 , HIS H:94 , HOH H:302 , HOH H:305 , HOH H:349
binding site for residue FUC H 201
26
AE8
SOFTWARE
GLN A:16 , ILE A:17 , TYR A:18 , ASN A:44 , GLY A:45 , ALA A:46 , ILE A:47 , PHE A:48 , PRO A:93 , HIS A:94 , HOH A:366 , GLN E:3 , FUC E:208
binding site for Poly-Saccharide residues GLC A 205 through FUC A 209
27
AE9
SOFTWARE
GLN A:16 , ILE A:17 , TYR A:18 , ASN A:44 , GLY A:45 , ALA A:46 , ILE A:47 , PHE A:48 , PRO A:93 , HIS A:94 , HOH A:366 , GLN C:3 , GLN D:16 , ILE D:17 , TYR D:18 , ASN D:44 , GLY D:45 , ALA D:46 , ILE D:47 , PHE D:48 , PRO D:93 , HIS D:94 , GLC D:210 , HOH D:301 , HOH D:304 , HOH D:305 , HOH D:306 , HOH D:308 , HOH D:313 , HOH D:315 , HOH D:320 , HOH D:321 , HOH D:322 , HOH D:333 , HOH D:337 , HOH D:350 , HOH D:357 , HOH D:366 , HOH D:386 , GLN E:3 , FUC E:208 , THR I:6 , ASN I:21 , GLU I:83 , LYS I:84 , HOH I:301
binding site for Poly-Saccharide residues BGC D 205 through FUC D 209
28
AF1
SOFTWARE
LYS A:43 , ASN A:44 , GLY A:45 , GLC A:205 , GLN C:3 , GLN D:3 , GLN D:16 , ILE D:17 , TYR D:18 , ASN D:44 , GLY D:45 , ALA D:46 , ILE D:47 , PHE D:48 , PRO D:93 , HIS D:94 , GLC D:210 , HOH D:301 , HOH D:304 , HOH D:305 , HOH D:306 , HOH D:308 , HOH D:313 , HOH D:315 , HOH D:320 , HOH D:321 , HOH D:322 , HOH D:333 , HOH D:337 , HOH D:350 , HOH D:357 , HOH D:366 , HOH D:386 , GLN E:16 , ILE E:17 , TYR E:18 , ASN E:44 , GLY E:45 , ALA E:46 , ILE E:47 , PHE E:48 , PRO E:93 , HIS E:94 , HOH E:315 , HOH E:375 , THR I:6 , ASN I:21 , GLU I:83 , LYS I:84 , HOH I:301
binding site for Poly-Saccharide residues GLC E 205 through FUC E 209
29
AF2
SOFTWARE
LYS A:43 , ASN A:44 , GLY A:45 , GLC A:205 , GLN E:16 , ILE E:17 , TYR E:18 , ASN E:44 , GLY E:45 , ALA E:46 , ILE E:47 , GLU E:79 , HIS E:94 , BCN E:201 , FUC E:209 , HOH E:303 , HOH E:315 , HOH E:375 , GLN F:16 , ILE F:17 , TYR F:18 , ASN F:44 , GLY F:45 , ALA F:46 , ILE F:47 , PHE F:48 , ALA F:80 , LYS F:81 , PRO F:93 , HIS F:94 , ASN F:103 , HOH F:302 , HOH F:310 , HOH F:316 , HOH F:317 , HOH F:318 , HOH F:326 , HOH F:385 , HOH F:391 , TYR G:76 , LEU G:77 , GLU G:79 , HOH G:304 , HOH G:312 , HOH G:340 , GLN J:3
binding site for Poly-Saccharide residues BGC F 202 through FUC F 206
30
AF3
SOFTWARE
GLN F:3 , GLN F:16 , ILE F:17 , TYR F:18 , ASN F:44 , GLY F:45 , ALA F:46 , ILE F:47 , PHE F:48 , PRO F:93 , HIS F:94 , HOH F:302 , HOH F:310 , HOH F:316 , HOH F:317 , HOH F:318 , HOH F:326 , HOH F:385 , HOH F:391 , GLN G:16 , ILE G:17 , TYR G:18 , ASN G:44 , GLY G:45 , ALA G:46 , ILE G:47 , PHE G:48 , THR G:92 , PRO G:93 , HIS G:94 , BGC G:201 , HOH G:301 , HOH G:302 , HOH G:303 , HOH G:308 , HOH G:321 , HOH G:345 , HOH G:356 , HOH G:386 , HOH G:389 , HOH G:392 , HOH G:395 , THR I:1 , GLN J:3 , SER J:55 , GLN J:56 , ASN J:90 , LYS J:91 , THR J:92 , HOH J:327
binding site for Poly-Saccharide residues GAL G 202 through GLC G 206
31
AF4
SOFTWARE
GLN F:3 , ASP F:59 , LYS F:63 , GLN G:16 , ILE G:17 , TYR G:18 , ASN G:44 , GLY G:45 , ALA G:46 , ILE G:47 , PHE G:48 , ASP G:59 , THR G:92 , PRO G:93 , HIS G:94 , HOH G:301 , HOH G:302 , HOH G:303 , HOH G:308 , HOH G:321 , HOH G:331 , HOH G:345 , HOH G:356 , HOH G:386 , HOH G:389 , HOH G:392 , HOH G:395 , GLN H:3 , THR I:1 , GLN I:16 , TYR I:18 , ASN I:44 , GLY I:45 , ALA I:46 , ILE I:47 , PRO I:93 , HIS I:94 , HOH I:303 , HOH I:305 , HOH I:320 , HOH I:322 , HOH I:358 , HOH I:362 , HOH I:363 , HOH I:385 , HOH I:389 , HOH I:396 , SER J:55 , GLN J:56 , ASN J:90 , LYS J:91 , THR J:92 , HOH J:327
binding site for Poly-Saccharide residues GLC I 201 through FUC I 205
32
AF5
SOFTWARE
LYS D:84 , HOH D:332 , ASP F:59 , LYS F:63 , ASP G:59 , GLN H:3 , GLN I:3 , GLN I:16 , TYR I:18 , ASN I:44 , GLY I:45 , ALA I:46 , ILE I:47 , PRO I:93 , HIS I:94 , HOH I:303 , HOH I:305 , HOH I:320 , HOH I:322 , HOH I:358 , HOH I:362 , HOH I:363 , HOH I:385 , HOH I:389 , HOH I:396 , GLN J:16 , ILE J:17 , TYR J:18 , ASN J:44 , GLY J:45 , ALA J:46 , ILE J:47 , PHE J:48 , THR J:92 , PRO J:93 , HIS J:94 , HOH J:302 , HOH J:303 , HOH J:304 , HOH J:305 , HOH J:306 , HOH J:309 , HOH J:312 , HOH J:329 , HOH J:372 , HOH J:376 , HOH J:377 , HOH J:379 , HOH J:396 , HOH J:403
binding site for Poly-Saccharide residues GLC J 201 through FUC J 205
[
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
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
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 (218 KB)
Header - Asym.Unit
Biol.Unit 1 (106 KB)
Header - Biol.Unit 1
Biol.Unit 2 (107 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
5ELF
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
