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3G0D
Biol. Unit 1
Info
Asym.Unit (520 KB)
Biol.Unit 1 (262 KB)
Biol.Unit 2 (256 KB)
Biol.Unit 3 (136 KB)
Biol.Unit 4 (135 KB)
Biol.Unit 5 (134 KB)
Biol.Unit 6 (131 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIPEPTIDYL PEPTIDASE IV IN COMPLEX WITH A PYRIMIDINEDIONE INHIBITOR 2
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
:
2.39
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, 16)
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)
1w: N-ACETYL-D-GLUCOSAMINE (NAGw)
1x: N-ACETYL-D-GLUCOSAMINE (NAGx)
2a: 2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]... (XIHa)
2b: 2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]... (XIHb)
2c: 2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]... (XIHc)
2d: 2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]... (XIHd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
XIH
2
Ligand/Ion
2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]-1,3-DIMETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-7H-PURIN-7-YL}METHYL)BENZONITRILE
[
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Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:125 , GLU A:205 , GLU A:206 , TYR A:547 , TRP A:629 , SER A:630 , TYR A:631 , TYR A:662 , TYR A:666 , HOH A:866 , HOH A:933 , HOH A:1010
BINDING SITE FOR RESIDUE XIH A 800
02
AC2
SOFTWARE
VAL A:78 , 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 , NAG A:805
BINDING SITE FOR RESIDUE NAG A 804
06
AC6
SOFTWARE
NAG A:804
BINDING SITE FOR RESIDUE NAG A 805
07
AC7
SOFTWARE
TRP A:187 , ASN A:281 , NAG A:807 , HOH A:1079 , HOH A:1080
BINDING SITE FOR RESIDUE NAG A 806
08
AC8
SOFTWARE
TRP A:187 , NAG A:806 , HOH A:1079
BINDING SITE FOR RESIDUE NAG A 807
09
AC9
SOFTWARE
ASN A:321 , SER A:349 , THR A:350 , HOH A:833
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 , VAL B:711 , HOH B:830 , HOH B:906 , HOH B:948
BINDING SITE FOR RESIDUE XIH B 800
11
BC2
SOFTWARE
TYR B:83 , ASN B:85 , SER B:87 , HOH B:1063
BINDING SITE FOR RESIDUE NAG B 801
12
BC3
SOFTWARE
ILE B:148 , ASN B:150 , HOH B:1026
BINDING SITE FOR RESIDUE NAG B 802
13
BC4
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309 , HOH B:901
BINDING SITE FOR RESIDUE NAG B 803
14
BC5
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , NAG B:805
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
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
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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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_d3g0da1 (A:41-508)
1b: SCOP_d3g0db1 (B:36-508)
1c: SCOP_d3g0dc1 (C:41-508)
1d: SCOP_d3g0dd1 (D:41-508)
2a: SCOP_d3g0da2 (A:509-766)
2b: SCOP_d3g0db2 (B:509-766)
2c: SCOP_d3g0dc2 (C:509-766)
2d: SCOP_d3g0dd2 (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
d3g0da1
A:41-508
1b
d3g0db1
B:36-508
1c
d3g0dc1
C:41-508
1d
d3g0dd1
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
d3g0da2
A:509-766
2b
d3g0db2
B:509-766
2c
d3g0dc2
C:509-766
2d
d3g0dd2
D:509-766
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3g0dA02 (A:509-766)
1b: CATH_3g0dB02 (B:509-766)
1c: CATH_3g0dC02 (C:509-766)
1d: CATH_3g0dD02 (D:509-766)
2a: CATH_3g0dA01 (A:41-508)
2b: CATH_3g0dC01 (C:41-508)
2c: CATH_3g0dD01 (D:41-508)
2d: CATH_3g0dB01 (B:36-508)
View:
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)
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
3g0dA02
A:509-766
1b
3g0dB02
B:509-766
1c
3g0dC02
C:509-766
1d
3g0dD02
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
3g0dA01
A:41-508
2b
3g0dC01
C:41-508
2c
3g0dD01
D:41-508
2d
3g0dB01
B:36-508
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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