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3G0G
Biol. Unit 2
Info
Asym.Unit (508 KB)
Biol.Unit 1 (264 KB)
Biol.Unit 2 (242 KB)
Biol.Unit 3 (129 KB)
Biol.Unit 4 (144 KB)
Biol.Unit 5 (128 KB)
Biol.Unit 6 (123 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIPEPTIDYL PEPTIDASE IV IN COMPLEX WITH A PYRIMIDINONE INHIBITOR 3
Authors
:
Z. Zhang, M. B. Wallace, J. Feng, J. A. Stafford, S. W. Kaldor, L. Shi, R. J K. Aertgeerts, B. Lee, A. Jennings, R. Xu, D. Kassel, D. R. Webb, S. L. Gw
Date
:
27 Jan 09 (Deposition) - 16 Feb 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A (1x)
Biol. Unit 4: B (1x)
Biol. Unit 5: C (1x)
Biol. Unit 6: D (1x)
Keywords
:
Dpp4, Pyrimidinone, Pyrimidindione, Aminopeptidase, Cell Membrane, Glycoprotein, Hydrolase, Membrane, Protease, Secreted, Serine Protease, Signal-Anchor, Transmembrane, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Zhang, M. B. Wallace, J. Feng, J. A. Stafford, R. J. Skene, L. Shi, B. Lee, K. Aertgeerts, A. Jennings, R. Xu, D. B. Kassel, S. W. Kaldor, M. Navre, D. R. Webb, S. L. Gwaltney
Design And Synthesis Of Pyrimidinone And Pyrimidinedione Inhibitors Of Dipeptidyl Peptidase Iv.
J. Med. Chem. V. 54 510 2011
[
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Hetero Components
(2, 9)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
1ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
1ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
1ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
1ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
1af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
1q: N-ACETYL-D-GLUCOSAMINE (NAGq)
1r: N-ACETYL-D-GLUCOSAMINE (NAGr)
1s: N-ACETYL-D-GLUCOSAMINE (NAGs)
1t: N-ACETYL-D-GLUCOSAMINE (NAGt)
1u: N-ACETYL-D-GLUCOSAMINE (NAGu)
1v: N-ACETYL-D-GLUCOSAMINE (NAGv)
1w: N-ACETYL-D-GLUCOSAMINE (NAGw)
1x: N-ACETYL-D-GLUCOSAMINE (NAGx)
1y: N-ACETYL-D-GLUCOSAMINE (NAGy)
1z: N-ACETYL-D-GLUCOSAMINE (NAGz)
2a: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (RUMa)
2b: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (RUMb)
2c: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (RUMc)
2d: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (RUMd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
RUM
1
Ligand/Ion
2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]-5-BROMO-6-OXOPYRIMIDIN-1(6H)-YL}METHYL)BENZONITRILE
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: CC1 (SOFTWARE)
02: CC2 (SOFTWARE)
03: CC3 (SOFTWARE)
04: CC4 (SOFTWARE)
05: CC5 (SOFTWARE)
06: CC6 (SOFTWARE)
07: CC7 (SOFTWARE)
08: CC8 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC2 (SOFTWARE)
12: DC3 (SOFTWARE)
13: DC4 (SOFTWARE)
14: DC5 (SOFTWARE)
15: DC6 (SOFTWARE)
16: DC7 (SOFTWARE)
17: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC1
SOFTWARE
HOH B:1115 , HOH B:1278 , ARG C:125 , GLU C:205 , GLU C:206 , TYR C:547 , TRP C:629 , SER C:630 , TYR C:631 , VAL C:656 , TYR C:662 , TYR C:666 , ASN C:710 , VAL C:711
BINDING SITE FOR RESIDUE RUM C 800
02
CC2
SOFTWARE
ASN C:85 , SER C:87
BINDING SITE FOR RESIDUE NAG C 801
03
CC3
SOFTWARE
ASN C:150
BINDING SITE FOR RESIDUE NAG C 802
04
CC4
SOFTWARE
ASN C:219 , THR C:221 , GLN C:308
BINDING SITE FOR RESIDUE NAG C 803
05
CC5
SOFTWARE
ILE C:194 , ASN C:229 , THR C:231 , GLU C:232 , LYS C:267 , NAG C:805
BINDING SITE FOR RESIDUE NAG C 804
06
CC6
SOFTWARE
NAG C:804
BINDING SITE FOR RESIDUE NAG C 805
07
CC7
SOFTWARE
ASN C:281 , NAG C:807
BINDING SITE FOR RESIDUE NAG C 806
08
CC8
SOFTWARE
TRP C:187 , NAG C:806
BINDING SITE FOR RESIDUE NAG C 807
09
CC9
SOFTWARE
ASN C:321 , SER C:349
BINDING SITE FOR RESIDUE NAG C 808
10
DC1
SOFTWARE
HOH B:1277 , ARG D:125 , GLU D:205 , GLU D:206 , TYR D:547 , SER D:630 , TYR D:631 , VAL D:656 , TYR D:662 , TYR D:666 , VAL D:711
BINDING SITE FOR RESIDUE RUM D 800
11
DC2
SOFTWARE
ILE D:148 , ASN D:150
BINDING SITE FOR RESIDUE NAG D 802
12
DC3
SOFTWARE
HOH B:1254 , ASN D:219 , GLY D:220 , THR D:221 , ASP D:274 , GLN D:308
BINDING SITE FOR RESIDUE NAG D 803
13
DC4
SOFTWARE
ILE D:194 , GLN D:227 , ASN D:229 , THR D:231 , GLU D:232 , NAG D:805
BINDING SITE FOR RESIDUE NAG D 804
14
DC5
SOFTWARE
THR D:231 , NAG D:804
BINDING SITE FOR RESIDUE NAG D 805
15
DC6
SOFTWARE
ASN D:281 , NAG D:807
BINDING SITE FOR RESIDUE NAG D 806
16
DC7
SOFTWARE
NAG D:806
BINDING SITE FOR RESIDUE NAG D 807
17
DC8
SOFTWARE
ARG D:317 , ILE D:319 , ASN D:321 , TYR D:322
BINDING SITE FOR RESIDUE NAG D 808
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PRO_ENDOPEP_SER (C:605-635,D:605-635)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PRO_ENDOPEP_SER
PS00708
Prolyl endopeptidase family serine active site.
DPP4_HUMAN
605-635
2
-
-
C:605-635
D:605-635
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3g0ga1 (A:41-508)
1b: SCOP_d3g0gb1 (B:35-508)
1c: SCOP_d3g0gc1 (C:41-508)
1d: SCOP_d3g0gd1 (D:41-508)
2a: SCOP_d3g0ga2 (A:509-766)
2b: SCOP_d3g0gb2 (B:509-766)
2c: SCOP_d3g0gc2 (C:509-766)
2d: SCOP_d3g0gd2 (D:509-766)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
DPP6 N-terminal domain-like
(99)
Family
:
DPP6 N-terminal domain-like
(99)
Protein domain
:
Dipeptidyl peptidase IV/CD26, N-terminal domain
(88)
Human (Homo sapiens) [TaxId: 9606]
(80)
1a
d3g0ga1
A:41-508
1b
d3g0gb1
B:35-508
1c
d3g0gc1
C:41-508
1d
d3g0gd1
D:41-508
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
automated matches
(184)
Protein domain
:
automated matches
(184)
Human (Homo sapiens) [TaxId: 9606]
(42)
2a
d3g0ga2
A:509-766
2b
d3g0gb2
B:509-766
2c
d3g0gc2
C:509-766
2d
d3g0gd2
D:509-766
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3g0gA02 (A:509-766)
1b: CATH_3g0gB02 (B:509-766)
1c: CATH_3g0gC02 (C:509-766)
1d: CATH_3g0gD02 (D:509-766)
2a: CATH_3g0gA01 (A:41-508)
2b: CATH_3g0gC01 (C:41-508)
2c: CATH_3g0gB01 (B:35-508)
2d: CATH_3g0gD01 (D:41-508)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1820, no name defined]
(692)
Human (Homo sapiens)
(118)
1a
3g0gA02
A:509-766
1b
3g0gB02
B:509-766
1c
3g0gC02
C:509-766
1d
3g0gD02
D:509-766
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.30, no name defined]
(74)
Human (Homo sapiens)
(59)
2a
3g0gA01
A:41-508
2b
3g0gC01
C:41-508
2c
3g0gB01
B:35-508
2d
3g0gD01
D:41-508
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (508 KB)
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