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3G0C
Biol. Unit 4
Info
Asym.Unit (504 KB)
Biol.Unit 1 (254 KB)
Biol.Unit 2 (249 KB)
Biol.Unit 3 (131 KB)
Biol.Unit 4 (132 KB)
Biol.Unit 5 (130 KB)
Biol.Unit 6 (128 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIPEPTIDYL PEPTIDASE IV IN COMPLEX WITH A PYRIMIDINEDIONE INHIBITOR 1
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) - 02 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.69
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, 7)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
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)
2a: 7-(2-CHLOROBENZYL)-1,3-DIMETHYL-8-... (RUFa)
2b: 7-(2-CHLOROBENZYL)-1,3-DIMETHYL-8-... (RUFb)
2c: 7-(2-CHLOROBENZYL)-1,3-DIMETHYL-8-... (RUFc)
2d: 7-(2-CHLOROBENZYL)-1,3-DIMETHYL-8-... (RUFd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
RUF
1
Ligand/Ion
7-(2-CHLOROBENZYL)-1,3-DIMETHYL-8-PIPERAZIN-1-YL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE
[
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Sites
(7, 7)
Info
All Sites
1: BC1 (SOFTWARE)
2: BC2 (SOFTWARE)
3: BC3 (SOFTWARE)
4: BC4 (SOFTWARE)
5: BC5 (SOFTWARE)
6: BC6 (SOFTWARE)
7: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
BC1
SOFTWARE
GLU B:205 , GLU B:206 , TYR B:547 , SER B:630 , TYR B:631 , TYR B:662 , TYR B:666 , ASN B:710 , VAL B:711 , HIS B:740
BINDING SITE FOR RESIDUE RUF B 800
2
BC2
SOFTWARE
ASN B:85 , HOH B:889
BINDING SITE FOR RESIDUE NAG B 801
3
BC3
SOFTWARE
ILE B:148 , ASN B:150
BINDING SITE FOR RESIDUE NAG B 802
4
BC4
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309
BINDING SITE FOR RESIDUE NAG B 803
5
BC5
SOFTWARE
ASN B:229 , THR B:231 , NAG B:805
BINDING SITE FOR RESIDUE NAG B 804
6
BC6
SOFTWARE
NAG B:804
BINDING SITE FOR RESIDUE NAG B 805
7
BC7
SOFTWARE
ASN B:281
BINDING SITE FOR RESIDUE NAG B 806
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PRO_ENDOPEP_SER (B:605-635)
;
View:
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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
1
-
B:605-635
-
-
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Exons
(0, 0)
Info
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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_d3g0ca1 (A:41-508)
1b: SCOP_d3g0cb1 (B:36-508)
1c: SCOP_d3g0cc1 (C:41-508)
1d: SCOP_d3g0cd1 (D:41-508)
2a: SCOP_d3g0ca2 (A:509-766)
2b: SCOP_d3g0cb2 (B:509-766)
2c: SCOP_d3g0cc2 (C:509-766)
2d: SCOP_d3g0cd2 (D:509-766)
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(
)
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
d3g0ca1
A:41-508
1b
d3g0cb1
B:36-508
1c
d3g0cc1
C:41-508
1d
d3g0cd1
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
d3g0ca2
A:509-766
2b
d3g0cb2
B:509-766
2c
d3g0cc2
C:509-766
2d
d3g0cd2
D:509-766
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3g0cA02 (A:509-766)
1b: CATH_3g0cB02 (B:509-766)
1c: CATH_3g0cC02 (C:509-766)
1d: CATH_3g0cD02 (D:509-766)
2a: CATH_3g0cA01 (A:41-508)
2b: CATH_3g0cC01 (C:41-508)
2c: CATH_3g0cD01 (D:41-508)
2d: CATH_3g0cB01 (B:36-508)
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)
(
)
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
3g0cA02
A:509-766
1b
3g0cB02
B:509-766
1c
3g0cC02
C:509-766
1d
3g0cD02
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
3g0cA01
A:41-508
2b
3g0cC01
C:41-508
2c
3g0cD01
D:41-508
2d
3g0cB01
B:36-508
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain B
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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Asym.Unit (504 KB)
Header - Asym.Unit
Biol.Unit 1 (254 KB)
Header - Biol.Unit 1
Biol.Unit 2 (249 KB)
Header - Biol.Unit 2
Biol.Unit 3 (131 KB)
Header - Biol.Unit 3
Biol.Unit 4 (132 KB)
Header - Biol.Unit 4
Biol.Unit 5 (130 KB)
Header - Biol.Unit 5
Biol.Unit 6 (128 KB)
Header - Biol.Unit 6
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