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2AJ8
Asym. Unit
Info
Asym.Unit (539 KB)
Biol.Unit 1 (268 KB)
Biol.Unit 2 (269 KB)
Biol.Unit 3 (526 KB)
Biol.Unit 4 (528 KB)
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Title
:
PORCINE DIPEPTIDYL PEPTIDASE IV (CD26) IN COMPLEX WITH 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-1-YL-3,7-DIHYDRO-PURINE-2,6-DIONE (BDPX)
Authors
:
M. Engel, T. Hoffmann, S. Manhart, U. Heiser, S. Chambre, R. Huber, H. U. W. Bode
Date
:
01 Aug 05 (Deposition) - 28 Feb 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.11
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Biol. Unit 4: A,B,C,D (1x)
Keywords
:
Serine Protease, Dipeptidyl Peptidase, Oxyanion Hole, Substrate Channeling, Drug Design, Diabetes Mellitus, Flexibility, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Engel, T. Hoffmann, S. Manhart, U. Heiser, S. Chambre, R. Huber, H. U. Demuth, W. Bode
Rigidity And Flexibility Of Dipeptidyl Peptidase Iv: Crysta Structures Of And Docking Experiments With Dpiv.
J. Mol. Biol. V. 355 768 2006
[
close entry info
]
Hetero Components
(4, 47)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
2ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
2ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
2ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
2ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
2af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
2ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
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)
2y: N-ACETYL-D-GLUCOSAMINE (NAGy)
2z: N-ACETYL-D-GLUCOSAMINE (NAGz)
3a: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-... (SC3a)
3b: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-... (SC3b)
3c: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-... (SC3c)
3d: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-... (SC3d)
3e: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-... (SC3e)
3f: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-... (SC3f)
3g: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-... (SC3g)
3h: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-... (SC3h)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
NAG
33
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SC3
8
Ligand/Ion
7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-1-YL-3,7-DIHYDRO-PURINE-2,6-DIONE
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(47, 47)
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: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:78 , ASN A:85 , SER A:87 , HOH A:1761
BINDING SITE FOR RESIDUE NAG A 767A
02
AC2
SOFTWARE
GLU A:73 , ASN A:74 , ASN A:75 , ASN A:92
BINDING SITE FOR RESIDUE NAG A 768A
03
AC3
SOFTWARE
GLN A:227 , ASN A:229 , THR A:231 , GLU A:232 , LYS A:267 , NAG A:770B , HOH A:1788 , HOH A:1957 , HOH A:1989
BINDING SITE FOR RESIDUE NAG A 769A
04
AC4
SOFTWARE
NAG A:769A , HOH A:1691
BINDING SITE FOR RESIDUE NAG A 770B
05
AC5
SOFTWARE
ASN A:279
BINDING SITE FOR RESIDUE NAG A 771A
06
AC6
SOFTWARE
ASN A:321 , SER A:349 , ASP A:678 , HOH A:1655
BINDING SITE FOR RESIDUE NAG A 772A
07
AC7
SOFTWARE
ARG A:597 , GLY A:599 , THR A:600 , MET A:638 , TYR A:682 , ASN A:685 , ARG A:691 , NAG A:774B , HOH A:1630 , HOH A:1712 , HOH A:1901
BINDING SITE FOR RESIDUE NAG A 773A
08
AC8
SOFTWARE
ARG A:597 , TYR A:682 , NAG A:773A , HOH A:1841 , HOH A:1874 , HOH A:1901 , HOH A:1945
BINDING SITE FOR RESIDUE NAG A 774B
09
AC9
SOFTWARE
ASN B:85 , SER B:87
BINDING SITE FOR RESIDUE NAG B 767A
10
BC1
SOFTWARE
GLU B:73 , ASN B:74 , ASN B:75 , ASN B:92 , NAG B:769B , NAG B:773A
BINDING SITE FOR RESIDUE NAG B 768A
11
BC2
SOFTWARE
GLU B:73 , ILE B:348 , THR B:350 , NAG B:768A , BMA B:770C , HOH B:1909 , HOH B:2084
BINDING SITE FOR RESIDUE NAG B 769B
12
BC3
SOFTWARE
NAG B:769B
BINDING SITE FOR RESIDUE BMA B 770C
13
BC4
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , HOH B:1813 , HOH B:1891 , HOH B:1949
BINDING SITE FOR RESIDUE NAG B 771A
14
BC5
SOFTWARE
PRO B:278 , ASN B:279 , HOH B:1636 , HOH B:1761 , HOH B:1886 , HOH B:1898 , HOH B:2017 , VAL D:288 , HOH D:1965
BINDING SITE FOR RESIDUE NAG B 772A
15
BC6
SOFTWARE
ASN B:321 , SER B:349 , THR B:350 , NAG B:768A , HOH B:1834
BINDING SITE FOR RESIDUE NAG B 773A
16
BC7
SOFTWARE
ARG B:597 , GLY B:599 , THR B:600 , ASN B:685 , ARG B:691 , NAG B:775B , HOH B:1696 , HOH B:1767 , HOH B:1828
BINDING SITE FOR RESIDUE NAG B 774A
17
BC8
SOFTWARE
ARG B:597 , TYR B:682 , NAG B:774A
BINDING SITE FOR RESIDUE NAG B 775B
18
BC9
SOFTWARE
LEU C:78 , ASN C:85 , SER C:86 , SER C:87 , HOH C:1678
BINDING SITE FOR RESIDUE NAG C 767A
19
CC1
SOFTWARE
GLU C:73 , ASN C:74 , ASN C:92 , HOH C:1999
BINDING SITE FOR RESIDUE NAG C 768A
20
CC2
SOFTWARE
ILE C:194 , GLN C:227 , ASN C:229 , THR C:231 , GLU C:232 , LYS C:267 , HOH C:1819 , HOH C:1872
BINDING SITE FOR RESIDUE NAG C 769A
21
CC3
SOFTWARE
VAL A:288 , HOH A:1689 , HOH A:1978 , ASN C:279
BINDING SITE FOR RESIDUE NAG C 770A
22
CC4
SOFTWARE
ASN C:321 , SER C:349 , ARG C:596 , HOH C:1726 , HOH C:1868
BINDING SITE FOR RESIDUE NAG C 771A
23
CC5
SOFTWARE
ARG C:597 , GLY C:599 , THR C:600 , ASN C:685 , ARG C:691 , NAG C:773B , HOH C:1633 , HOH C:1772 , HOH C:1983
BINDING SITE FOR RESIDUE NAG C 772A
24
CC6
SOFTWARE
ARG C:597 , GLU C:604 , TYR C:682 , NAG C:772A , HOH C:1772
BINDING SITE FOR RESIDUE NAG C 773B
25
CC7
SOFTWARE
ASN D:85 , SER D:86 , SER D:87
BINDING SITE FOR RESIDUE NAG D 767A
26
CC8
SOFTWARE
GLU D:73 , ASN D:74 , ASN D:75 , ASN D:92 , NAG D:769B
BINDING SITE FOR RESIDUE NAG D 768A
27
CC9
SOFTWARE
GLU D:73 , NAG D:768A , BMA D:770C
BINDING SITE FOR RESIDUE NAG D 769B
28
DC1
SOFTWARE
GLU D:378 , NAG D:769B
BINDING SITE FOR RESIDUE BMA D 770C
29
DC2
SOFTWARE
ILE D:194 , GLN D:227 , ASN D:229 , THR D:231 , GLU D:232 , LYS D:267 , NAG D:772B
BINDING SITE FOR RESIDUE NAG D 771A
30
DC3
SOFTWARE
NAG D:771A
BINDING SITE FOR RESIDUE NAG D 772B
31
DC4
SOFTWARE
ASN D:279 , HOH D:1717
BINDING SITE FOR RESIDUE NAG D 773A
32
DC5
SOFTWARE
ASN D:321 , SER D:349 , ARG D:596 , NAG D:775B , HOH D:1828 , HOH D:1867
BINDING SITE FOR RESIDUE NAG D 774A
33
DC6
SOFTWARE
ARG D:596 , GLU D:677 , ASP D:678 , NAG D:774A
BINDING SITE FOR RESIDUE NAG D 775B
34
DC7
SOFTWARE
ARG D:597 , GLY D:599 , THR D:600 , MET D:638 , ASN D:685 , ARG D:691 , NAG D:777B , HOH D:1744 , HOH D:1947
BINDING SITE FOR RESIDUE NAG D 776A
35
DC8
SOFTWARE
ARG D:597 , GLU D:604 , TYR D:682 , NAG D:776A , HOH D:1947
BINDING SITE FOR RESIDUE NAG D 777B
36
DC9
SOFTWARE
ALA A:360 , GLU A:361 , HIS A:363 , GLY A:406 , ILE A:407 , HOH A:1631 , HOH A:1793 , HOH A:1812 , HOH A:1848 , HOH A:1851
BINDING SITE FOR RESIDUE SO4 A 1500
37
EC1
SOFTWARE
ALA B:360 , GLU B:361 , HIS B:363 , ILE B:374 , GLY B:406 , ILE B:407 , HOH B:1627 , HOH B:1642 , HOH B:1656 , HOH B:1922 , HOH B:1931 , HOH B:2064
BINDING SITE FOR RESIDUE SO4 B 1501
38
EC2
SOFTWARE
ALA C:360 , GLU C:361 , HIS C:363 , ILE C:374 , GLY C:406 , ILE C:407 , HOH C:1621 , HOH C:1671 , HOH C:1811
BINDING SITE FOR RESIDUE SO4 C 1502
39
EC3
SOFTWARE
ALA D:360 , GLU D:361 , HIS D:363 , ILE D:374 , GLY D:406 , ILE D:407 , HOH D:1652 , HOH D:1675 , HOH D:1962
BINDING SITE FOR RESIDUE SO4 D 1503
40
EC4
SOFTWARE
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 , VAL A:711
BINDING SITE FOR RESIDUE SC3 A 1601
41
EC5
SOFTWARE
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
BINDING SITE FOR RESIDUE SC3 B 1602
42
EC6
SOFTWARE
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 , VAL C:711
BINDING SITE FOR RESIDUE SC3 C 1603
43
EC7
SOFTWARE
GLU D:205 , GLU D:206 , TYR D:547 , TRP D:629 , SER D:630 , TYR D:631 , VAL D:656 , TYR D:662 , TYR D:666 , VAL D:711
BINDING SITE FOR RESIDUE SC3 D 1604
44
EC8
SOFTWARE
TRP B:187 , ALA B:280 , SER B:281 , VAL B:282 , PHE D:269 , SER D:284 , SC3 D:1606
BINDING SITE FOR RESIDUE SC3 B 1605
45
EC9
SOFTWARE
PHE B:269 , SER B:284 , SC3 B:1605 , TRP D:187 , ALA D:280 , SER D:281 , VAL D:282 , HOH D:1612
BINDING SITE FOR RESIDUE SC3 D 1606
46
FC1
SOFTWARE
PHE A:269 , SER A:284 , SC3 A:1608 , TRP C:187 , ALA C:280 , SER C:281 , VAL C:282
BINDING SITE FOR RESIDUE SC3 C 1607
47
FC2
SOFTWARE
TRP A:187 , ALA A:280 , SER A:281 , VAL A:282 , HOH A:1868 , SC3 C:1607
BINDING SITE FOR RESIDUE SC3 A 1608
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PRO_ENDOPEP_SER (A:605-635,B:605-635,C:605-635,D:60...)
;
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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
4
A:605-635
B:605-635
C:605-635
D: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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2aj8a1 (A:39-508)
1b: SCOP_d2aj8c1 (C:39-508)
1c: SCOP_d2aj8d1 (D:39-508)
1d: SCOP_d2aj8b1 (B:39-508)
2a: SCOP_d2aj8a2 (A:509-766)
2b: SCOP_d2aj8c2 (C:509-766)
2c: SCOP_d2aj8d2 (D:509-766)
2d: SCOP_d2aj8b2 (B:509-766)
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Protein Domains
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Organisms
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(
)
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
d2aj8a1
A:39-508
1b
d2aj8c1
C:39-508
1c
d2aj8d1
D:39-508
1d
d2aj8b1
B: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
d2aj8a2
A:509-766
2b
d2aj8c2
C:509-766
2c
d2aj8d2
D:509-766
2d
d2aj8b2
B:509-766
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2aj8A02 (A:509-766)
1b: CATH_2aj8B02 (B:509-766)
1c: CATH_2aj8C02 (C:509-766)
1d: CATH_2aj8D02 (D:509-766)
2a: CATH_2aj8A01 (A:39-508)
2b: CATH_2aj8C01 (C:39-508)
2c: CATH_2aj8D01 (D:39-508)
2d: CATH_2aj8B01 (B:39-508)
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Organisms
(
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(
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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
2aj8A02
A:509-766
1b
2aj8B02
B:509-766
1c
2aj8C02
C:509-766
1d
2aj8D02
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
2aj8A01
A:39-508
2b
2aj8C01
C:39-508
2c
2aj8D01
D:39-508
2d
2aj8B01
B:39-508
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Pfam Domains
(0, 0)
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all PFAM domains
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (539 KB)
Header - Asym.Unit
Biol.Unit 1 (268 KB)
Header - Biol.Unit 1
Biol.Unit 2 (269 KB)
Header - Biol.Unit 2
Biol.Unit 3 (526 KB)
Header - Biol.Unit 3
Biol.Unit 4 (528 KB)
Header - Biol.Unit 4
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