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3G0G
Biol. Unit 1
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
[
close entry info
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Hetero Components
(2, 18)
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
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
RUM
2
Ligand/Ion
2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]-5-BROMO-6-OXOPYRIMIDIN-1(6H)-YL}METHYL)BENZONITRILE
[
close Hetero Component info
]
Sites
(21, 21)
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: DC1 (SOFTWARE)
21: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:2 , ARG A:125 , GLU A:205 , GLU A:206 , TYR A:547 , TRP A:629 , SER A:630 , TYR A:631 , VAL A:656 , TYR A:662 , TYR A:666 , ASN A:710 , HOH B:1116 , HOH B:1336
BINDING SITE FOR RESIDUE RUM A 800
02
AC2
SOFTWARE
ASN A:85 , SER A:86 , SER A:87
BINDING SITE FOR RESIDUE NAG A 801
03
AC3
SOFTWARE
ASN A:150
BINDING SITE FOR RESIDUE NAG A 802
04
AC4
SOFTWARE
ASN A:219 , THR A:221 , GLN A:308 , GLU A:309
BINDING SITE FOR RESIDUE NAG A 803
05
AC5
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , NAG A:805
BINDING SITE FOR RESIDUE NAG A 804
06
AC6
SOFTWARE
NAG A:804 , HOH B:775
BINDING SITE FOR RESIDUE NAG A 805
07
AC7
SOFTWARE
TRP A:187 , ASN A:281 , NAG A:807
BINDING SITE FOR RESIDUE NAG A 806
08
AC8
SOFTWARE
NAG A:806
BINDING SITE FOR RESIDUE NAG A 807
09
AC9
SOFTWARE
ILE A:319 , ASN A:321 , SER A:349 , ARG A:596
BINDING SITE FOR RESIDUE NAG A 808
10
BC1
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , TYR B:547 , TRP B:629 , SER B:630 , TYR B:631 , VAL B:656 , TYR B:662 , TYR B:666 , ASN B:710 , VAL B:711 , HOH B:1042 , HOH B:1202 , HOH B:1203
BINDING SITE FOR RESIDUE RUM B 800
11
BC2
SOFTWARE
ASN B:85 , SER B:87
BINDING SITE FOR RESIDUE NAG B 801
12
BC3
SOFTWARE
ASN B:150
BINDING SITE FOR RESIDUE NAG B 802
13
BC4
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309 , HOH B:1402
BINDING SITE FOR RESIDUE NAG B 803
14
BC5
SOFTWARE
ASN B:229 , THR B:231 , NAG B:805 , HOH B:1273
BINDING SITE FOR RESIDUE NAG B 804
15
BC6
SOFTWARE
NAG B:804
BINDING SITE FOR RESIDUE NAG B 805
16
BC7
SOFTWARE
ASN B:281 , NAG B:807 , HOH B:1274 , HOH B:1275
BINDING SITE FOR RESIDUE NAG B 806
17
BC8
SOFTWARE
NAG B:806
BINDING SITE FOR RESIDUE NAG B 807
18
BC9
SOFTWARE
ILE B:319 , ASN B:321 , SER B:349
BINDING SITE FOR RESIDUE NAG B 808
19
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
20
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
21
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
[
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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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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PRO_ENDOPEP_SER (A:605-635,B: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
A:605-635
B:605-635
-
-
[
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Exons
(0, 0)
Info
All Exons
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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
(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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(
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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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