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2BUC
Biol. Unit 1
Info
Asym.Unit (515 KB)
Biol.Unit 1 (256 KB)
Biol.Unit 2 (258 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PORCINE DIPEPTIDYL PEPTIDASE IV (CD26) IN COMPLEX WITH A TETRAHYDROISOQUINOLINE INHIBITOR
Authors
:
S. Nordhoff, S. Cerezo-Galvez, A. Feurer, O. Hill, V. G. Matassa, G. Metz, C. Rummey, M. Thiemann, P. J. Edwards
Date
:
09 Jun 05 (Deposition) - 23 Jan 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Hydrolase/Inhibitor, Complex (Hydrolase/Inhibitor), Dpp-Iv, Diabetes Mellitus, Drug Design, Hydrolase, Serine Protease, Aminopeptidase, Glycoprotein, Protease, Signal- Anchor, Transmembrane, Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Nordhoff, S. Cerezo-Galvez, A. Feurer, O. Hill, V. G. Matassa, G. Metz, C. Rummey, M. Thiemann, P. J. Edwards
The Reversed Binding Of B-Phenethylamine Inhibitors Of Dpp-Iv. X-Ray Structures And Properties Of Novel Fragment And Elaborated Inhibitors.
Bioorg. Med. Chem. Lett. V. 16 1744 2006
[
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Hetero Components
(4, 22)
Info
All Hetero Components
1a: (S)-2-[(R)-3-AMINO-4-(2-FLUORO-PHE... (008a)
1b: (S)-2-[(R)-3-AMINO-4-(2-FLUORO-PHE... (008b)
1c: (S)-2-[(R)-3-AMINO-4-(2-FLUORO-PHE... (008c)
1d: (S)-2-[(R)-3-AMINO-4-(2-FLUORO-PHE... (008d)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
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)
3a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
3b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
3c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
3d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
3e: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGe)
3f: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGf)
3g: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGg)
3h: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGh)
3i: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGi)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
008
2
Ligand/Ion
(S)-2-[(R)-3-AMINO-4-(2-FLUORO-PHENYL)-BUTYRYL]-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID AMIDE
2
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(24, 24)
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: CC2 (SOFTWARE)
18: DC2 (SOFTWARE)
19: DC7 (SOFTWARE)
20: DC8 (SOFTWARE)
21: DC9 (SOFTWARE)
22: EC1 (SOFTWARE)
23: EC6 (SOFTWARE)
24: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:85 , SER A:87 , HOH A:2225 , HOH A:2226
BINDING SITE FOR RESIDUE NAG A1085
02
AC2
SOFTWARE
GLU A:73 , ASN A:74 , ASN A:75 , ASN A:92 , GLY A:521 , HOH A:2228
BINDING SITE FOR RESIDUE NAG A1092
03
AC3
SOFTWARE
ILE A:194 , GLN A:227 , ASN A:229 , THR A:231 , GLU A:232 , LYS A:267 , NAG A:1230 , HOH A:2232
BINDING SITE FOR RESIDUE NAG A1229
04
AC4
SOFTWARE
NAG A:1229 , HOH A:2232 , HOH A:2233
BINDING SITE FOR RESIDUE NAG A1230
05
AC5
SOFTWARE
ASN A:279 , TYR C:285 , HOH C:2089
BINDING SITE FOR RESIDUE NAG A1279
06
AC6
SOFTWARE
THR A:144 , ASN A:321 , SER A:349 , THR A:350 , HOH A:2118 , HOH A:2235 , HOH A:2236
BINDING SITE FOR RESIDUE NAG A1321
07
AC7
SOFTWARE
GLY A:599 , THR A:600 , ASN A:685 , ARG A:691 , NDG A:1686 , HOH A:2238 , HOH A:2239 , HOH A:2240
BINDING SITE FOR RESIDUE NDG A1685
08
AC8
SOFTWARE
ARG A:597 , NDG A:1685 , HOH A:2240
BINDING SITE FOR RESIDUE NDG A1686
09
AC9
SOFTWARE
ASN B:85 , SER B:86 , SER B:87
BINDING SITE FOR RESIDUE NAG B1085
10
BC1
SOFTWARE
GLU B:73 , ASN B:75 , ASN B:92 , ILE B:348 , NAG B:1093
BINDING SITE FOR RESIDUE NAG B1092
11
BC2
SOFTWARE
GLU B:73 , THR B:350 , NAG B:1092
BINDING SITE FOR RESIDUE NAG B1093
12
BC3
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , LYS B:267 , HOH B:2089 , HOH B:2242 , HOH B:2243
BINDING SITE FOR RESIDUE NAG B1229
13
BC4
SOFTWARE
ASN B:279 , HOH B:2244 , HOH B:2245 , VAL D:288
BINDING SITE FOR RESIDUE NAG B1279
14
BC5
SOFTWARE
ASN B:321 , SER B:349 , THR B:350 , HOH B:2134 , HOH B:2246
BINDING SITE FOR RESIDUE NAG B1321
15
BC6
SOFTWARE
ARG B:597 , GLY B:599 , THR B:600 , ASN B:685 , ARG B:691 , NAG B:1686 , HOH B:2211
BINDING SITE FOR RESIDUE NAG B1685
16
BC7
SOFTWARE
ARG B:597 , TYR B:682 , NAG B:1685 , HOH B:2211 , HOH B:2247
BINDING SITE FOR RESIDUE NAG B1686
17
CC2
SOFTWARE
VAL A:288 , HOH A:2087 , ASN C:279 , HOH C:2222
BINDING SITE FOR RESIDUE NAG C1279
18
DC2
SOFTWARE
TYR B:285 , HOH B:2104 , ASN D:279 , HOH D:2088 , HOH D:2224 , HOH D:2225
BINDING SITE FOR RESIDUE NDG D1279
19
DC7
SOFTWARE
ALA A:360 , GLU A:361 , HIS A:363 , ILE A:374 , GLY A:406 , ILE A:407 , HOH A:2122
BINDING SITE FOR RESIDUE SO4 A1768
20
DC8
SOFTWARE
ARG A:125 , TYR A:547 , SER A:630 , HIS A:740 , 008 A:1767 , HOH A:2242
BINDING SITE FOR RESIDUE SO4 A1769
21
DC9
SOFTWARE
ALA B:360 , GLU B:361 , HIS B:363 , ILE B:374 , GLY B:406 , ILE B:407 , HOH B:2140 , HOH B:2248
BINDING SITE FOR RESIDUE SO4 B1768
22
EC1
SOFTWARE
ARG B:125 , TYR B:547 , SER B:630 , HIS B:740 , 008 B:1767
BINDING SITE FOR RESIDUE SO4 B1769
23
EC6
SOFTWARE
ARG A:125 , GLU A:205 , GLU A:206 , VAL A:207 , SER A:209 , PHE A:357 , TYR A:547 , SER A:630 , TYR A:662 , TYR A:666 , ASN A:710 , VAL A:711 , HIS A:740 , SO4 A:1769 , HOH A:2161 , HOH A:2241
BINDING SITE FOR RESIDUE 008 A1767
24
EC7
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , VAL B:207 , SER B:209 , PHE B:357 , ARG B:358 , TYR B:547 , TYR B:662 , TYR B:666 , ASN B:710 , VAL B:711 , HIS B:740 , SO4 B:1769 , HOH B:2189
BINDING SITE FOR RESIDUE 008 B1767
[
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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_PIG
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_d2buca1 (A:39-508)
1b: SCOP_d2bucb1 (B:39-508)
1c: SCOP_d2bucc1 (C:39-508)
1d: SCOP_d2bucd1 (D:39-508)
2a: SCOP_d2buca2 (A:509-766)
2b: SCOP_d2bucb2 (B:509-766)
2c: SCOP_d2bucc2 (C:509-766)
2d: SCOP_d2bucd2 (D:509-766)
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)
(
)
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(
)
(
)
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)
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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)
Pig (Sus scrofa) [TaxId: 9823]
(8)
1a
d2buca1
A:39-508
1b
d2bucb1
B:39-508
1c
d2bucc1
C:39-508
1d
d2bucd1
D:39-508
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
DPP6 catalytic domain-like
(63)
Protein domain
:
Dipeptidyl peptidase IV/CD26, C-terminal domain
(62)
Pig (Sus scrofa) [TaxId: 9823]
(8)
2a
d2buca2
A:509-766
2b
d2bucb2
B:509-766
2c
d2bucc2
C:509-766
2d
d2bucd2
D:509-766
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2bucA02 (A:509-766)
1b: CATH_2bucB02 (B:509-766)
1c: CATH_2bucC02 (C:509-766)
1d: CATH_2bucD02 (D:509-766)
2a: CATH_2bucA01 (A:39-508)
2b: CATH_2bucB01 (B:39-508)
2c: CATH_2bucC01 (C:39-508)
2d: CATH_2bucD01 (D:39-508)
View:
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Topologies
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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)
Pig (Sus scrofa)
(22)
1a
2bucA02
A:509-766
1b
2bucB02
B:509-766
1c
2bucC02
C:509-766
1d
2bucD02
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)
Pig (Sus scrofa)
(8)
2a
2bucA01
A:39-508
2b
2bucB01
B:39-508
2c
2bucC01
C:39-508
2d
2bucD01
D:39-508
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Asym.Unit (515 KB)
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