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.
5KBY
Biol. Unit 3
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (516 KB)
Biol.Unit 2 (515 KB)
Biol.Unit 3 (1022 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 DIPEPTIDYL PEPTIDASE IV IN COMPLEX WITH SYR-472
Authors
:
R. J. Skene, A. J. Jennings
Date
:
03 Jun 16 (Deposition) - 13 Jul 16 (Release) - 07 Sep 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.24
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Peptidase, Glp-1, Metabolic Disease, Co-Complex, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. E. Grimshaw, A. Jennings, R. Kamran, H. Ueno, N. Nishigaki, T. Kosaka, A. Tani, H. Sano, Y. Kinugawa, E. Koumura, L. Shi, K. Takeuch
Trelagliptin (Syr-472, Zafatek), Novel Once-Weekly Treatmen For Type 2 Diabetes, Inhibits Dipeptidyl Peptidase-4 (Dpp-4 Via A Non-Covalent Mechanism.
Plos One V. 11 57509 2016
[
close entry info
]
Hetero Components
(2, 18)
Info
All Hetero Components
1a: 2-[[6-[(3~{R})-3-AZANYLPIPERIDIN-1... (6RLa)
1b: 2-[[6-[(3~{R})-3-AZANYLPIPERIDIN-1... (6RLb)
1c: 2-[[6-[(3~{R})-3-AZANYLPIPERIDIN-1... (6RLc)
1d: 2-[[6-[(3~{R})-3-AZANYLPIPERIDIN-1... (6RLd)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
2m: N-ACETYL-D-GLUCOSAMINE (NAGm)
2n: N-ACETYL-D-GLUCOSAMINE (NAGn)
2o: N-ACETYL-D-GLUCOSAMINE (NAGo)
2p: N-ACETYL-D-GLUCOSAMINE (NAGp)
2q: N-ACETYL-D-GLUCOSAMINE (NAGq)
2r: N-ACETYL-D-GLUCOSAMINE (NAGr)
2s: N-ACETYL-D-GLUCOSAMINE (NAGs)
2t: N-ACETYL-D-GLUCOSAMINE (NAGt)
2u: N-ACETYL-D-GLUCOSAMINE (NAGu)
2v: N-ACETYL-D-GLUCOSAMINE (NAGv)
2w: N-ACETYL-D-GLUCOSAMINE (NAGw)
2x: N-ACETYL-D-GLUCOSAMINE (NAGx)
2y: N-ACETYL-D-GLUCOSAMINE (NAGy)
2z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6RL
2
Ligand/Ion
2-[[6-[(3~{R})-3-AZANYLPIPERIDIN-1-YL]-3-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]METHYL]-4-FLUORANYL-BENZENECARBONITRILE
2
NAG
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(26, 26)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:125 , GLU A:205 , GLU A:206 , TYR A:547 , SER A:630 , TYR A:631 , VAL A:656 , TRP A:659 , TYR A:662 , TYR A:666 , VAL A:711 , HOH A:1674 , HOH A:1906
binding site for residue 6RL A 1510
02
AC2
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , TYR B:547 , SER B:630 , TYR B:631 , VAL B:656 , TRP B:659 , TYR B:662 , TYR B:666 , ASN B:710 , VAL B:711 , HOH B:1001
binding site for residue 6RL B 808
03
AC3
SOFTWARE
ARG C:125 , GLU C:205 , GLU C:206 , TYR C:547 , SER C:630 , TYR C:631 , VAL C:656 , TRP C:659 , TYR C:662 , TYR C:666 , VAL C:711 , HOH C:1632
binding site for residue 6RL C 1506
04
AC4
SOFTWARE
ARG D:125 , GLU D:205 , GLU D:206 , TYR D:547 , SER D:630 , TYR D:631 , VAL D:656 , TRP D:659 , TYR D:662 , TYR D:666 , ASN D:710 , VAL D:711 , HOH D:1720 , HOH D:1862
binding site for residue 6RL D 1507
05
AC5
SOFTWARE
ASN A:85 , SER A:86 , SER A:87
binding site for Mono-Saccharide NAG A 1509 bound to ASN A 85
06
AC6
SOFTWARE
ARG A:147 , ASN A:150 , HOH A:1720 , HOH A:1844
binding site for Poly-Saccharide residues NAG A 1501 through NAG A 1502 bound to ASN A 150
07
AC7
SOFTWARE
ASN A:219 , THR A:221 , GLN A:308 , GLU A:309
binding site for Mono-Saccharide NAG A 1503 bound to ASN A 219
08
AC8
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232
binding site for Poly-Saccharide residues NAG A 1504 through NAG A 1505 bound to ASN A 229
09
AC9
SOFTWARE
TRP A:187 , VAL A:279 , ASN A:281 , HOH A:1609
binding site for Poly-Saccharide residues NAG A 1506 through NAG A 1507 bound to ASN A 281
10
AD1
SOFTWARE
ILE A:319 , ASN A:321 , SER A:349 , THR A:350 , ARG A:596
binding site for Mono-Saccharide NAG A 1508 bound to ASN A 321
11
AD2
SOFTWARE
TYR B:83 , ASN B:85 , SER B:86 , SER B:87 , HOH B:949 , HOH B:1152
binding site for Mono-Saccharide NAG B 801 bound to ASN B 85
12
AD3
SOFTWARE
ASN B:150 , HOH B:958
binding site for Mono-Saccharide NAG B 802 bound to ASN B 150
13
AD4
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309 , HOH B:901 , HOH B:1036
binding site for Mono-Saccharide NAG B 807 bound to ASN B 219
14
AD5
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , HOH B:1037
binding site for Poly-Saccharide residues NAG B 803 through NAG B 804 bound to ASN B 229
15
AD6
SOFTWARE
VAL B:279 , ASN B:281
binding site for Mono-Saccharide NAG B 805 bound to ASN B 281
16
AD7
SOFTWARE
ILE B:319 , ASN B:321 , MET B:348 , SER B:349 , THR B:350 , ARG B:596 , HOH B:939
binding site for Mono-Saccharide NAG B 806 bound to ASN B 321
17
AD8
SOFTWARE
ILE C:148 , ASN C:150 , HOH C:1799
binding site for Mono-Saccharide NAG C 1501 bound to ASN C 150
18
AD9
SOFTWARE
ASN C:229 , THR C:231 , GLU C:232 , HOH C:1601
binding site for Poly-Saccharide residues NAG C 1502 through NAG C 1503 bound to ASN C 229
19
AE1
SOFTWARE
ASN C:281
binding site for Mono-Saccharide NAG C 1504 bound to ASN C 281
20
AE2
SOFTWARE
ILE C:319 , ASN C:321 , SER C:349 , ARG C:596
binding site for Mono-Saccharide NAG C 1505 bound to ASN C 321
21
AE3
SOFTWARE
ILE C:319 , ASN C:321 , SER C:349 , ARG C:596
binding site for Mono-Saccharide NAG C 1505 bound to ASN C 321
22
AE4
SOFTWARE
ARG D:147 , ASN D:150 , HOH D:1775 , HOH D:1824
binding site for Mono-Saccharide NAG D 1501 bound to ASN D 150
23
AE5
SOFTWARE
ASN D:219 , THR D:221 , GLN D:308 , GLU D:309 , HOH D:1618
binding site for Mono-Saccharide NAG D 1502 bound to ASN D 219
24
AE6
SOFTWARE
ASN D:229 , THR D:231 , GLU D:232 , LYS D:267 , HOH D:1687 , HOH D:1723 , HOH D:1828
binding site for Poly-Saccharide residues NAG D 1503 through NAG D 1504 bound to ASN D 229
25
AE7
SOFTWARE
VAL D:279 , ASN D:281 , HOH D:1718
binding site for Mono-Saccharide NAG D 1505 bound to ASN D 281
26
AE8
SOFTWARE
ILE D:319 , ASN D:321 , SER D:349 , ARG D:596
binding site for Mono-Saccharide NAG D 1506 bound to ASN D 321
[
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 B
Chain C
Chain D
Asymmetric Unit 1
Asymmetric Unit 2
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 (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (516 KB)
Header - Biol.Unit 1
Biol.Unit 2 (515 KB)
Header - Biol.Unit 2
Biol.Unit 3 (1022 KB)
Header - Biol.Unit 3
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
5KBY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
