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2BUA
Biol. Unit 2
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
[
close entry info
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Hetero Components
(4, 23)
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
2
Ligand/Ion
1-METHYLAMINE-1-BENZYL-CYCLOPENTANE
2
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
NDG
7
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC5 (SOFTWARE)
02: BC4 (SOFTWARE)
03: BC8 (SOFTWARE)
04: BC9 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC6 (SOFTWARE)
11: CC7 (SOFTWARE)
12: CC8 (SOFTWARE)
13: CC9 (SOFTWARE)
14: DC1 (SOFTWARE)
15: DC2 (SOFTWARE)
16: DC3 (SOFTWARE)
17: DC4 (SOFTWARE)
18: DC5 (SOFTWARE)
19: DC6 (SOFTWARE)
20: EC2 (SOFTWARE)
21: EC3 (SOFTWARE)
22: EC4 (SOFTWARE)
23: EC5 (SOFTWARE)
24: EC8 (SOFTWARE)
25: EC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
ASN A:279 , TYR C:285 , HOH C:2072
BINDING SITE FOR RESIDUE NAG A1279
02
BC4
SOFTWARE
ASN B:279 , TYR D:285 , VAL D:288
BINDING SITE FOR RESIDUE NAG B1279
03
BC8
SOFTWARE
MET B:616 , LEU C:78 , ASN C:85 , SER C:87
BINDING SITE FOR RESIDUE NAG C1085
04
BC9
SOFTWARE
GLU C:73 , ASN C:74 , ASN C:75 , ASN C:92
BINDING SITE FOR RESIDUE NDG C1092
05
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
06
CC2
SOFTWARE
VAL A:288 , ASN C:279
BINDING SITE FOR RESIDUE NAG C1279
07
CC3
SOFTWARE
ASN C:321 , SER C:349 , ASP C:678 , HOH C:2205
BINDING SITE FOR RESIDUE NAG C1321
08
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
09
CC5
SOFTWARE
ARG C:597 , TYR C:682 , NAG C:1685 , HOH C:2206
BINDING SITE FOR RESIDUE NDG C1686
10
CC6
SOFTWARE
ASN D:85 , SER D:87
BINDING SITE FOR RESIDUE NDG D1085
11
CC7
SOFTWARE
GLU D:73 , ASN D:75 , ASN D:92 , ILE D:348 , NAG D:1093
BINDING SITE FOR RESIDUE NDG D1092
12
CC8
SOFTWARE
GLU D:73 , NDG D:1092
BINDING SITE FOR RESIDUE NAG D1093
13
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
14
DC1
SOFTWARE
GLU D:232 , NDG D:1229
BINDING SITE FOR RESIDUE NAG D1230
15
DC2
SOFTWARE
ASN D:279
BINDING SITE FOR RESIDUE NAG D1279
16
DC3
SOFTWARE
ALA D:319 , ASN D:321 , SER D:349 , THR D:350 , NDG D:1322
BINDING SITE FOR RESIDUE NDG D1321
17
DC4
SOFTWARE
ARG D:596 , ASP D:678 , NDG D:1321
BINDING SITE FOR RESIDUE NDG D1322
18
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
19
DC6
SOFTWARE
ARG D:597 , GLU D:604 , TYR D:682 , NAG D:1685
BINDING SITE FOR RESIDUE NAG D1686
20
EC2
SOFTWARE
ALA C:360 , GLU C:361 , HIS C:363 , ILE C:407 , HOH C:2207
BINDING SITE FOR RESIDUE SO4 C1768
21
EC3
SOFTWARE
ARG C:125 , TRP C:629 , SER C:630 , HIS C:740 , 007 C:1767
BINDING SITE FOR RESIDUE SO4 C1769
22
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
23
EC5
SOFTWARE
ARG D:125 , TRP D:629 , SER D:630 , HIS D:740 , 007 D:1767
BINDING SITE FOR RESIDUE SO4 D1769
24
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
25
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 only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PRO_ENDOPEP_SER (C:605-635,D: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
-
-
C:605-635
D:605-635
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_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)
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)
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)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
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)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (518 KB)
Header - Asym.Unit
Biol.Unit 1 (258 KB)
Header - Biol.Unit 1
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