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2AJB
Asym. Unit
Info
Asym.Unit (520 KB)
Biol.Unit 1 (258 KB)
Biol.Unit 2 (261 KB)
Biol.Unit 3 (510 KB)
Biol.Unit 4 (509 KB)
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(1)
Title
:
PORCINE DIPEPTIDYL PEPTIDASE IV (CD26) IN COMPLEX WITH THE TRIPEPTIDE TERT-BUTYL-GLY-L-PRO-L-ILE (TBU-GPI)
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
:
2.75
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, Alpha/Beta-Hydrolase, Beta- Propeller, Oxyanion Hole, Substrate Channeling, Drug Design, Diabetes Mellitus, Flexibility, Hydrolase-Hydrolase Inhibitor Complex
(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
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Hetero Components
(4, 43)
Info
All Hetero Components
1a: 3-METHYL-L-VALYL-L-PROLYL-L-ISOLEU... (0QGa)
1b: 3-METHYL-L-VALYL-L-PROLYL-L-ISOLEU... (0QGb)
1c: 3-METHYL-L-VALYL-L-PROLYL-L-ISOLEU... (0QGc)
1d: 3-METHYL-L-VALYL-L-PROLYL-L-ISOLEU... (0QGd)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
3ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
3ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
3ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
3ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
3af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
3ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
3x: N-ACETYL-D-GLUCOSAMINE (NAGx)
3y: N-ACETYL-D-GLUCOSAMINE (NAGy)
3z: N-ACETYL-D-GLUCOSAMINE (NAGz)
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
0QG
4
Ligand/Ion
3-METHYL-L-VALYL-L-PROLYL-L-ISOLEUCINE
2
BMA
2
Ligand/Ion
BETA-D-MANNOSE
3
NAG
33
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(34, 34)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:125 , GLU A:205 , GLU A:206 , TYR A:547 , SER A:630 , TYR A:631 , VAL A:656 , TYR A:662 , TYR A:666 , ASN A:710 , HIS A:740
BINDING SITE FOR RESIDUE 0QG A 802
02
AC2
SOFTWARE
LEU A:78 , ASN A:85 , SER A:86 , SER A:87 , HOH A:1570
BINDING SITE FOR RESIDUE NAG A 767A
03
AC3
SOFTWARE
ASN A:75 , ASN A:92 , GLY A:521
BINDING SITE FOR RESIDUE NAG A 768A
04
AC4
SOFTWARE
ASN A:279 , HOH A:1573
BINDING SITE FOR RESIDUE NAG A 771A
05
AC5
SOFTWARE
ASN A:321 , ILE A:348 , SER A:349 , THR A:350 , ASP A:678 , HOH A:1523 , HOH A:1555
BINDING SITE FOR RESIDUE NAG A 772A
06
AC6
SOFTWARE
ALA A:360 , GLU A:361 , HIS A:363 , ILE A:374 , GLY A:406 , ILE A:407 , HOH A:1547 , HOH A:1550 , HOH A:1587 , HOH A:1629
BINDING SITE FOR RESIDUE SO4 A 1500
07
AC7
SOFTWARE
ARG B:125 , 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
BINDING SITE FOR RESIDUE 0QG B 802
08
AC8
SOFTWARE
LEU B:78 , ASN B:85 , SER B:86 , SER B:87 , HOH B:1576 , HOH B:1677
BINDING SITE FOR RESIDUE NAG B 767A
09
AC9
SOFTWARE
ILE B:194 , ASN B:229 , GLU B:232 , HOH B:1510 , HOH B:1609
BINDING SITE FOR RESIDUE NAG B 771A
10
BC1
SOFTWARE
ASN B:279 , HOH B:1521 , TYR D:285 , VAL D:288 , LEU D:294
BINDING SITE FOR RESIDUE NAG B 772A
11
BC2
SOFTWARE
ASN B:321 , SER B:349 , THR B:350 , HOH B:1583 , HOH B:1639 , HOH B:1663 , HOH B:1670
BINDING SITE FOR RESIDUE NAG B 773A
12
BC3
SOFTWARE
ALA B:360 , GLU B:361 , HIS B:363 , GLY B:406 , ILE B:407 , HOH B:1503 , HOH B:1674
BINDING SITE FOR RESIDUE SO4 B 1501
13
BC4
SOFTWARE
ARG C:125 , GLU C:205 , GLU C:206 , TYR C:547 , SER C:630 , TYR C:631 , TYR C:662 , TYR C:666 , ASN C:710 , HIS C:740
BINDING SITE FOR RESIDUE 0QG C 802
14
BC5
SOFTWARE
LEU C:78 , ASN C:85 , SER C:87 , HOH C:1593
BINDING SITE FOR RESIDUE NAG C 767A
15
BC6
SOFTWARE
GLU C:73 , ASN C:74 , ASN C:75 , ASN C:92 , HOH C:1697
BINDING SITE FOR RESIDUE NAG C 768A
16
BC7
SOFTWARE
ILE C:194 , ASN C:229 , THR C:231 , GLU C:232 , HOH C:1528 , HOH C:1556 , HOH C:1646
BINDING SITE FOR RESIDUE NAG C 769A
17
BC8
SOFTWARE
VAL A:288 , ASN C:279 , HOH C:1599
BINDING SITE FOR RESIDUE NAG C 770A
18
BC9
SOFTWARE
ASN C:321 , SER C:349 , ARG C:596 , HOH C:1518 , HOH C:1653
BINDING SITE FOR RESIDUE NAG C 771A
19
CC1
SOFTWARE
ALA C:360 , GLU C:361 , HIS C:363 , GLY C:406 , ILE C:407 , HOH C:1523
BINDING SITE FOR RESIDUE SO4 C 1502
20
CC2
SOFTWARE
ARG D:125 , GLU D:205 , GLU D:206 , TYR D:547 , SER D:630 , TYR D:631 , TYR D:662 , TYR D:666 , ASN D:710 , VAL D:711 , HIS D:740
BINDING SITE FOR RESIDUE 0QG D 802
21
CC3
SOFTWARE
ASN D:85 , SER D:87
BINDING SITE FOR RESIDUE NAG D 767A
22
CC4
SOFTWARE
ASN D:279 , HOH D:1546 , HOH D:1670 , HOH D:1707
BINDING SITE FOR RESIDUE NAG D 773A
23
CC5
SOFTWARE
GLY D:599 , THR D:600 , MET D:638 , ASN D:685 , SER D:686 , ARG D:691 , NAG D:777B , HOH D:1514 , HOH D:1665
BINDING SITE FOR RESIDUE NAG D 776A
24
CC6
SOFTWARE
ARG D:597 , GLU D:604 , TYR D:682 , NAG D:776A , HOH D:1622 , HOH D:1685
BINDING SITE FOR RESIDUE NAG D 777B
25
CC7
SOFTWARE
ALA D:360 , GLU D:361 , HIS D:363 , GLY D:406 , ILE D:407 , HOH D:1550 , HOH D:1552 , HOH D:1600
BINDING SITE FOR RESIDUE SO4 D 1503
26
CC8
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , HOH A:1571 , HOH A:1605 , HOH A:1656
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 229 RESIDUES 769 TO 770
27
CC9
SOFTWARE
ARG A:597 , GLY A:599 , THR A:600 , MET A:638 , TYR A:682 , ASN A:685 , SER A:686 , ARG A:691 , HOH A:1567 , HOH A:1687
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 685 RESIDUES 773 TO 774
28
DC1
SOFTWARE
GLU B:73 , ASN B:74 , ASN B:75 , ASN B:92 , THR B:350 , HOH B:1703 , HOH B:1711 , HOH B:1715
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 92 RESIDUES 768 TO 770
29
DC2
SOFTWARE
ARG B:597 , THR B:600 , TYR B:682 , ASN B:685 , SER B:686 , ARG B:691 , HOH B:1706
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 685 RESIDUES 774 TO 775
30
DC3
SOFTWARE
ARG C:597 , GLY C:599 , THR C:600 , GLU C:604 , TYR C:682 , ASN C:685 , ARG C:691 , HOH C:1573 , HOH C:1610 , HOH C:1621 , HOH C:1633
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 685 RESIDUES 772 TO 773
31
DC4
SOFTWARE
GLU D:73 , ASN D:74 , ASN D:75 , ASN D:92 , ILE D:348 , GLU D:378 , HOH D:1602 , HOH D:1709
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 92 RESIDUES 768 TO 770
32
DC5
SOFTWARE
ASN D:229 , THR D:231 , GLU D:232 , HOH D:1710
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 229 RESIDUES 771 TO 772
33
DC6
SOFTWARE
ASN D:321 , SER D:349 , ARG D:596 , GLU D:677 , HOH D:1638 , HOH D:1696
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 321 RESIDUES 774 TO 775
34
DC7
SOFTWARE
ARG D:597 , GLY D:599 , THR D:600 , GLU D:604 , MET D:638 , TYR D:682 , ASN D:685 , SER D:686 , ARG D:691 , HOH D:1514 , HOH D:1622 , HOH D:1665 , HOH D:1685
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 685 RESIDUES 776 TO 777
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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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...)
;
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
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_d2ajba1 (A:39-508)
1b: SCOP_d2ajbb1 (B:39-508)
1c: SCOP_d2ajbc1 (C:39-508)
1d: SCOP_d2ajbd1 (D:39-508)
2a: SCOP_d2ajba2 (A:509-766)
2b: SCOP_d2ajbb2 (B:509-766)
2c: SCOP_d2ajbc2 (C:509-766)
2d: SCOP_d2ajbd2 (D:509-766)
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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
d2ajba1
A:39-508
1b
d2ajbb1
B:39-508
1c
d2ajbc1
C:39-508
1d
d2ajbd1
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
d2ajba2
A:509-766
2b
d2ajbb2
B:509-766
2c
d2ajbc2
C:509-766
2d
d2ajbd2
D:509-766
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2ajbA02 (A:509-766)
1b: CATH_2ajbB02 (B:509-766)
1c: CATH_2ajbC02 (C:509-766)
1d: CATH_2ajbD02 (D:509-766)
2a: CATH_2ajbA01 (A:39-508)
2b: CATH_2ajbB01 (B:39-508)
2c: CATH_2ajbC01 (C:39-508)
2d: CATH_2ajbD01 (D:39-508)
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Topologies
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Homologous Superfamilies
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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)
Pig (Sus scrofa)
(22)
1a
2ajbA02
A:509-766
1b
2ajbB02
B:509-766
1c
2ajbC02
C:509-766
1d
2ajbD02
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
2ajbA01
A:39-508
2b
2ajbB01
B:39-508
2c
2ajbC01
C:39-508
2d
2ajbD01
D:39-508
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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