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.
4K6T
Biol. Unit 2
Info
Asym.Unit (394 KB)
Biol.Unit 1 (195 KB)
Biol.Unit 2 (195 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 AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0385
Authors
:
T. Stehle, J. Bauer
Date
:
16 Apr 13 (Deposition) - 22 Oct 14 (Release) - 09 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,E,F,G
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: E,F,G (1x)
Keywords
:
Adenovirus, Fiber Knob, Protein Carbohydrate Interaction, Sialic Acid, Carbohydrate Mimic, Multivalent Ligand, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Caraballo, M. Saleeb, J. Bauer, A. M. Liaci, N. Chandra, R. J. Storm, L. Frangsmyr, W. Qian, T. Stehle, N. Arnberg, M. Elofsson
Triazole Linker-Based Trivalent Sialic Acid Inhibitors Of Adenovirus Type 37 Infection Of Human Corneal Epithelial Cells.
Org. Biomol. Chem. V. 13 9194 2015
[
close entry info
]
Hetero Components
(4, 18)
Info
All Hetero Components
1a: 2,2',2''-[NITRILOTRIS(METHANEDIYL-... (1P0a)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
2e: ACETATE ION (ACTe)
2f: ACETATE ION (ACTf)
2g: ACETATE ION (ACTg)
2h: ACETATE ION (ACTh)
2i: ACETATE ION (ACTi)
3a: CALCIUM ION (CAa)
4a: CHLORIDE ION (CLa)
5a: 1,2-ETHANEDIOL (EDOa)
5b: 1,2-ETHANEDIOL (EDOb)
5c: 1,2-ETHANEDIOL (EDOc)
5d: 1,2-ETHANEDIOL (EDOd)
5e: 1,2-ETHANEDIOL (EDOe)
5f: 1,2-ETHANEDIOL (EDOf)
5g: 1,2-ETHANEDIOL (EDOg)
5h: 1,2-ETHANEDIOL (EDOh)
5i: 1,2-ETHANEDIOL (EDOi)
5j: 1,2-ETHANEDIOL (EDOj)
5k: 1,2-ETHANEDIOL (EDOk)
5l: 1,2-ETHANEDIOL (EDOl)
5m: 1,2-ETHANEDIOL (EDOm)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
7c: MAGNESIUM ION (MGc)
7d: MAGNESIUM ION (MGd)
7e: MAGNESIUM ION (MGe)
7f: MAGNESIUM ION (MGf)
8a: O-SIALIC ACID (SIAa)
8b: O-SIALIC ACID (SIAb)
8c: O-SIALIC ACID (SIAc)
8d: O-SIALIC ACID (SIAd)
8e: O-SIALIC ACID (SIAe)
8f: O-SIALIC ACID (SIAf)
9a: ZINC ION (ZNa)
9b: ZINC ION (ZNb)
9c: ZINC ION (ZNc)
9d: ZINC ION (ZNd)
9e: ZINC ION (ZNe)
9f: ZINC ION (ZNf)
9g: ZINC ION (ZNg)
9h: ZINC ION (ZNh)
9i: ZINC ION (ZNi)
9j: ZINC ION (ZNj)
9k: ZINC ION (ZNk)
9l: ZINC ION (ZNl)
9m: ZINC ION (ZNm)
9n: ZINC ION (ZNn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1P0
-1
Ligand/Ion
2,2',2''-[NITRILOTRIS(METHANEDIYL-1H-1,2,3-TRIAZOLE-4,1-DIYL)]TRIETHANOL
2
ACT
5
Ligand/Ion
ACETATE ION
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
6
GOL
3
Ligand/Ion
GLYCEROL
7
MG
-1
Ligand/Ion
MAGNESIUM ION
8
SIA
3
Ligand/Ion
O-SIALIC ACID
9
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: BC4 (SOFTWARE)
02: BC7 (SOFTWARE)
03: CC8 (SOFTWARE)
04: CC9 (SOFTWARE)
05: DC1 (SOFTWARE)
06: DC2 (SOFTWARE)
07: DC3 (SOFTWARE)
08: DC4 (SOFTWARE)
09: DC5 (SOFTWARE)
10: DC6 (SOFTWARE)
11: DC7 (SOFTWARE)
12: DC8 (SOFTWARE)
13: DC9 (SOFTWARE)
14: EC1 (SOFTWARE)
15: EC2 (SOFTWARE)
16: EC3 (SOFTWARE)
17: EC4 (SOFTWARE)
18: EC5 (SOFTWARE)
19: EC6 (SOFTWARE)
20: EC7 (SOFTWARE)
21: EC8 (SOFTWARE)
22: EC9 (SOFTWARE)
23: FC1 (SOFTWARE)
24: FC2 (SOFTWARE)
25: FC3 (SOFTWARE)
26: FC4 (SOFTWARE)
27: FC5 (SOFTWARE)
28: FC6 (SOFTWARE)
29: FC7 (SOFTWARE)
30: FC8 (SOFTWARE)
31: FC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC4
SOFTWARE
ASP B:258 , SER F:299
BINDING SITE FOR RESIDUE ZN B 404
02
BC7
SOFTWARE
HIS B:231 , GLU B:351 , ZN B:403 , GLU E:281
BINDING SITE FOR RESIDUE ACT B 407
03
CC8
SOFTWARE
HIS E:231 , GLU E:351 , HOH E:588 , ACT F:404 , HOH F:602
BINDING SITE FOR RESIDUE ZN E 401
04
CC9
SOFTWARE
ASP E:318
BINDING SITE FOR RESIDUE ZN E 402
05
DC1
SOFTWARE
TYR E:312 , PRO E:317 , ASP E:318 , LYS E:345 , HOH E:531 , TYR F:308 , VAL F:322 , SER F:344 , HOH F:526
BINDING SITE FOR RESIDUE SIA E 403
06
DC2
SOFTWARE
GLU E:348 , ACT E:406
BINDING SITE FOR RESIDUE ACT E 404
07
DC3
SOFTWARE
LYS E:236 , ACT E:406
BINDING SITE FOR RESIDUE ACT E 405
08
DC4
SOFTWARE
LYS E:236 , GLU E:348 , ACT E:404 , ACT E:405
BINDING SITE FOR RESIDUE ACT E 406
09
DC5
SOFTWARE
LYS E:282 , ILE E:284 , GLY E:285
BINDING SITE FOR RESIDUE EDO E 407
10
DC6
SOFTWARE
LYS E:301 , LYS E:324 , THR E:326 , HOH E:613
BINDING SITE FOR RESIDUE EDO E 408
11
DC7
SOFTWARE
SER E:260 , HOH E:581
BINDING SITE FOR RESIDUE EDO E 409
12
DC8
SOFTWARE
GLU E:334 , GOL E:411
BINDING SITE FOR RESIDUE EDO E 410
13
DC9
SOFTWARE
GLY E:332 , CYS E:333 , EDO E:410
BINDING SITE FOR RESIDUE GOL E 411
14
EC1
SOFTWARE
LYS E:212 , GLU E:365 , HOH E:626 , HOH E:627
BINDING SITE FOR RESIDUE MG E 412
15
EC2
SOFTWARE
HIS F:231 , GLU F:351 , HOH F:621
BINDING SITE FOR RESIDUE ZN F 401
16
EC3
SOFTWARE
ASP F:318 , HOH F:627
BINDING SITE FOR RESIDUE ZN F 402
17
EC4
SOFTWARE
TYR F:312 , PRO F:317 , ASP F:318 , LYS F:345 , HOH F:573 , HOH F:606 , HOH F:618 , TYR G:308 , VAL G:322 , HOH G:638
BINDING SITE FOR RESIDUE SIA F 403
18
EC5
SOFTWARE
HIS E:231 , GLU E:351 , ZN E:401 , HOH E:588 , HOH E:594 , LYS F:300 , TYR F:302 , HOH F:602
BINDING SITE FOR RESIDUE ACT F 404
19
EC6
SOFTWARE
GLY F:228 , HIS F:231
BINDING SITE FOR RESIDUE EDO F 405
20
EC7
SOFTWARE
ILE F:284 , GLY F:285
BINDING SITE FOR RESIDUE EDO F 406
21
EC8
SOFTWARE
ASN F:195 , LYS F:202 , GLY F:263 , TYR F:266 , TRP F:267 , HOH F:537
BINDING SITE FOR RESIDUE EDO F 407
22
EC9
SOFTWARE
ASP F:201 , LYS F:202
BINDING SITE FOR RESIDUE MG F 408
23
FC1
SOFTWARE
LYS F:212 , GLU F:365 , HOH F:625
BINDING SITE FOR RESIDUE MG F 409
24
FC2
SOFTWARE
HIS G:231
BINDING SITE FOR RESIDUE ZN G 401
25
FC3
SOFTWARE
GLU G:351
BINDING SITE FOR RESIDUE ZN G 402
26
FC4
SOFTWARE
ASP G:318
BINDING SITE FOR RESIDUE ZN G 403
27
FC5
SOFTWARE
VAL E:322 , HOH E:610 , TYR G:312 , PRO G:317 , ASP G:318 , LYS G:345 , HOH G:633
BINDING SITE FOR RESIDUE SIA G 404
28
FC6
SOFTWARE
ASP F:182 , ARG F:270 , LYS G:212 , GLY G:214 , GLU G:365 , CA G:408
BINDING SITE FOR RESIDUE ACT G 405
29
FC7
SOFTWARE
GLN G:319 , ASN G:349 , GLU G:351 , HOH G:584 , HOH G:640
BINDING SITE FOR RESIDUE GOL G 406
30
FC8
SOFTWARE
ALA G:283 , ILE G:284 , GLY G:285 , HOH G:594
BINDING SITE FOR RESIDUE GOL G 407
31
FC9
SOFTWARE
LYS G:212 , GLU G:365 , ACT G:405
BINDING SITE FOR RESIDUE CA G 408
[
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 E
Chain F
Chain G
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 (394 KB)
Header - Asym.Unit
Biol.Unit 1 (195 KB)
Header - Biol.Unit 1
Biol.Unit 2 (195 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
4K6T
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help