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2BUA
Asym. Unit
Info
Asym.Unit (518 KB)
Biol.Unit 1 (258 KB)
Biol.Unit 2 (259 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PORCINE DIPEPTIDYL PEPTIDASE IV (CD26) IN COMPLEX WITH A LOW MOLECULAR WEIGHT 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
:
2.56
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Hydrolase/Inhibitor, Dpp-Iv, Diabetes Mellitus, Drug Design, Hydrolase, Serine Protease, Aminopeptidase, Glycoprotein, Protease, Signal- Anchor, Transmembrane, Complex (Hydrolase/Inhibitor)
(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, 45)
Info
All Hetero Components
1a: 1-METHYLAMINE-1-BENZYL-CYCLOPENTAN... (007a)
1b: 1-METHYLAMINE-1-BENZYL-CYCLOPENTAN... (007b)
1c: 1-METHYLAMINE-1-BENZYL-CYCLOPENTAN... (007c)
1d: 1-METHYLAMINE-1-BENZYL-CYCLOPENTAN... (007d)
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)
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)
3j: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGj)
3k: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGk)
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
007
4
Ligand/Ion
1-METHYLAMINE-1-BENZYL-CYCLOPENTANE
2
NAG
22
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
NDG
11
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(45, 45)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:80 , ASN A:85 , SER A:86 , SER A:87
BINDING SITE FOR RESIDUE NAG A1085
02
AC2
SOFTWARE
GLU A:73 , ASN A:75 , ASN A:92 , GLY A:521
BINDING SITE FOR RESIDUE NDG A1092
03
AC3
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , NAG A:1230
BINDING SITE FOR RESIDUE NAG A1229
04
AC4
SOFTWARE
NAG A:1229
BINDING SITE FOR RESIDUE NAG A1230
05
AC5
SOFTWARE
ASN A:279 , TYR C:285 , HOH C:2072
BINDING SITE FOR RESIDUE NAG A1279
06
AC6
SOFTWARE
THR A:144 , ASN A:321 , SER A:349 , ASP A:678
BINDING SITE FOR RESIDUE NAG A1321
07
AC7
SOFTWARE
GLY A:599 , THR A:600 , ASN A:685 , SER A:686 , ARG A:691 , NDG A:1686 , HOH A:2185
BINDING SITE FOR RESIDUE NDG A1685
08
AC8
SOFTWARE
GLY A:99 , TYR A:100 , ARG A:597 , TYR A:682 , NDG A:1685
BINDING SITE FOR RESIDUE NDG A1686
09
AC9
SOFTWARE
TYR B:83 , 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 NDG B1092
11
BC2
SOFTWARE
GLU B:73 , THR B:350 , NDG B:1092
BINDING SITE FOR RESIDUE NAG B1093
12
BC3
SOFTWARE
ASN B:229 , THR B:231 , HOH B:2247 , HOH B:2248
BINDING SITE FOR RESIDUE NAG B1229
13
BC4
SOFTWARE
ASN B:279 , TYR D:285 , VAL D:288
BINDING SITE FOR RESIDUE NAG B1279
14
BC5
SOFTWARE
ASN B:321 , ILE B:348 , SER B:349 , THR B:350 , HOH B:2249 , HOH B:2250 , HOH B:2251
BINDING SITE FOR RESIDUE NAG B1321
15
BC6
SOFTWARE
ARG B:597 , GLY B:599 , THR B:600 , ASN B:685 , SER B:686 , ARG B:691 , NAG B:1686 , HOH B:2252
BINDING SITE FOR RESIDUE NAG B1685
16
BC7
SOFTWARE
ARG B:597 , TYR B:682 , NAG B:1685
BINDING SITE FOR RESIDUE NAG B1686
17
BC8
SOFTWARE
MET B:616 , LEU C:78 , ASN C:85 , SER C:87
BINDING SITE FOR RESIDUE NAG C1085
18
BC9
SOFTWARE
GLU C:73 , ASN C:74 , ASN C:75 , ASN C:92
BINDING SITE FOR RESIDUE NDG C1092
19
CC1
SOFTWARE
ILE C:194 , ASN C:229 , THR C:231 , GLU C:232 , LYS C:267 , HOH C:2066
BINDING SITE FOR RESIDUE NAG C1229
20
CC2
SOFTWARE
VAL A:288 , ASN C:279
BINDING SITE FOR RESIDUE NAG C1279
21
CC3
SOFTWARE
ASN C:321 , SER C:349 , ASP C:678 , HOH C:2205
BINDING SITE FOR RESIDUE NAG C1321
22
CC4
SOFTWARE
THR C:600 , ASN C:685 , SER C:686 , ARG C:691 , NDG C:1686 , HOH C:2173 , HOH C:2206
BINDING SITE FOR RESIDUE NAG C1685
23
CC5
SOFTWARE
ARG C:597 , TYR C:682 , NAG C:1685 , HOH C:2206
BINDING SITE FOR RESIDUE NDG C1686
24
CC6
SOFTWARE
ASN D:85 , SER D:87
BINDING SITE FOR RESIDUE NDG D1085
25
CC7
SOFTWARE
GLU D:73 , ASN D:75 , ASN D:92 , ILE D:348 , NAG D:1093
BINDING SITE FOR RESIDUE NDG D1092
26
CC8
SOFTWARE
GLU D:73 , NDG D:1092
BINDING SITE FOR RESIDUE NAG D1093
27
CC9
SOFTWARE
GLN D:227 , ASN D:229 , THR D:231 , GLU D:232 , LYS D:267 , NAG D:1230
BINDING SITE FOR RESIDUE NDG D1229
28
DC1
SOFTWARE
GLU D:232 , NDG D:1229
BINDING SITE FOR RESIDUE NAG D1230
29
DC2
SOFTWARE
ASN D:279
BINDING SITE FOR RESIDUE NAG D1279
30
DC3
SOFTWARE
ALA D:319 , ASN D:321 , SER D:349 , THR D:350 , NDG D:1322
BINDING SITE FOR RESIDUE NDG D1321
31
DC4
SOFTWARE
ARG D:596 , ASP D:678 , NDG D:1321
BINDING SITE FOR RESIDUE NDG D1322
32
DC5
SOFTWARE
ARG D:597 , THR D:600 , MET D:638 , ASN D:685 , SER D:686 , ARG D:691 , NAG D:1686 , HOH D:2145
BINDING SITE FOR RESIDUE NAG D1685
33
DC6
SOFTWARE
ARG D:597 , GLU D:604 , TYR D:682 , NAG D:1685
BINDING SITE FOR RESIDUE NAG D1686
34
DC7
SOFTWARE
ALA A:360 , GLU A:361 , HIS A:363 , GLY A:406 , ILE A:407 , HOH A:2186
BINDING SITE FOR RESIDUE SO4 A1768
35
DC8
SOFTWARE
ARG A:125 , SER A:630 , HIS A:740 , 007 A:1767
BINDING SITE FOR RESIDUE SO4 A1769
36
DC9
SOFTWARE
ALA B:360 , GLU B:361 , HIS B:363 , GLY B:406 , ILE B:407 , HOH B:2253 , HOH B:2254
BINDING SITE FOR RESIDUE SO4 B1768
37
EC1
SOFTWARE
ARG B:125 , TRP B:629 , SER B:630 , HIS B:740 , 007 B:1767
BINDING SITE FOR RESIDUE SO4 B1769
38
EC2
SOFTWARE
ALA C:360 , GLU C:361 , HIS C:363 , ILE C:407 , HOH C:2207
BINDING SITE FOR RESIDUE SO4 C1768
39
EC3
SOFTWARE
ARG C:125 , TRP C:629 , SER C:630 , HIS C:740 , 007 C:1767
BINDING SITE FOR RESIDUE SO4 C1769
40
EC4
SOFTWARE
GLU D:361 , HIS D:363 , ILE D:374 , GLY D:406 , ILE D:407 , HOH D:2177 , HOH D:2178
BINDING SITE FOR RESIDUE SO4 D1768
41
EC5
SOFTWARE
ARG D:125 , TRP D:629 , SER D:630 , HIS D:740 , 007 D:1767
BINDING SITE FOR RESIDUE SO4 D1769
42
EC6
SOFTWARE
ARG A:125 , GLU A:205 , GLU A:206 , TYR A:547 , SER A:630 , TYR A:662 , TYR A:666 , SO4 A:1769
BINDING SITE FOR RESIDUE 007 A1767
43
EC7
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , TYR B:547 , SER B:630 , TYR B:662 , TYR B:666 , VAL B:711 , SO4 B:1769
BINDING SITE FOR RESIDUE 007 B1767
44
EC8
SOFTWARE
ARG C:125 , GLU C:205 , GLU C:206 , TYR C:547 , SER C:630 , TYR C:662 , TYR C:666 , VAL C:711 , SO4 C:1769
BINDING SITE FOR RESIDUE 007 C1767
45
EC9
SOFTWARE
GLU D:205 , GLU D:206 , TYR D:547 , SER D:630 , TYR D:662 , TYR D:666 , VAL D:711 , SO4 D:1769
BINDING SITE FOR RESIDUE 007 D1767
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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:
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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_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_d2buaa1 (A:39-508)
1b: SCOP_d2buab1 (B:39-508)
1c: SCOP_d2buac1 (C:39-508)
1d: SCOP_d2buad1 (D:39-508)
2a: SCOP_d2buaa2 (A:509-766)
2b: SCOP_d2buab2 (B:509-766)
2c: SCOP_d2buac2 (C:509-766)
2d: SCOP_d2buad2 (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)
Pig (Sus scrofa) [TaxId: 9823]
(8)
1a
d2buaa1
A:39-508
1b
d2buab1
B:39-508
1c
d2buac1
C:39-508
1d
d2buad1
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
d2buaa2
A:509-766
2b
d2buab2
B:509-766
2c
d2buac2
C:509-766
2d
d2buad2
D:509-766
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2buaA02 (A:509-766)
1b: CATH_2buaB02 (B:509-766)
1c: CATH_2buaC02 (C:509-766)
1d: CATH_2buaD02 (D:509-766)
2a: CATH_2buaA01 (A:39-508)
2b: CATH_2buaB01 (B:39-508)
2c: CATH_2buaC01 (C:39-508)
2d: CATH_2buaD01 (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
2buaA02
A:509-766
1b
2buaB02
B:509-766
1c
2buaC02
C:509-766
1d
2buaD02
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
2buaA01
A:39-508
2b
2buaB01
B:39-508
2c
2buaC01
C:39-508
2d
2buaD01
D:39-508
[
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Pfam Domains
(0, 0)
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all PFAM domains
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