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3W2T
Asym. Unit
Info
Asym.Unit (275 KB)
Biol.Unit 1 (267 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DEPIPTIDYL PEPTIDASE IV (DPP-4) IN COMPLEX WITH VILDAGLIPTIN
Authors
:
H. Kishida, M. Nabeno, I. Miyaguchi, Y. Tanaka, R. Katou, F. Akahoshi
Date
:
04 Dec 12 (Deposition) - 15 May 13 (Release) - 15 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.36
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Alpha/Beta, Beta-Propeller, Hydrolase, Aminopeptidase, Serine Protease, Secreted, Signal-Anchor, Transmembrane, Diabetes, Glycoprotein, Cell Membrane, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Nabeno, F. Akahoshi, H. Kishida, I. Miyaguchi, Y. Tanaka, S. Ishii, T. Kadowaki
A Comparative Study Of The Binding Modes Of Recently Launched Dipeptidyl Peptidase Iv Inhibitors In The Active Site
Biochem. Biophys. Res. Commun. V. 434 191 2013
[
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Hetero Components
(4, 25)
Info
All Hetero Components
1a: BETA-L-FUCOSE (FULa)
1b: BETA-L-FUCOSE (FULb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: (2S)-1-{N-[(1R,3S,5R,7S)-3-HYDROXY... (LF7a)
3b: (2S)-1-{N-[(1R,3S,5R,7S)-3-HYDROXY... (LF7b)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
4o: N-ACETYL-D-GLUCOSAMINE (NAGo)
4p: N-ACETYL-D-GLUCOSAMINE (NAGp)
4q: N-ACETYL-D-GLUCOSAMINE (NAGq)
4r: N-ACETYL-D-GLUCOSAMINE (NAGr)
4s: N-ACETYL-D-GLUCOSAMINE (NAGs)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUL
2
Ligand/Ion
BETA-L-FUCOSE
2
GOL
2
Ligand/Ion
GLYCEROL
3
LF7
2
Ligand/Ion
(2S)-1-{N-[(1R,3S,5R,7S)-3-HYDROXYTRICYCLO[3.3.1.1~3,7~]DEC-1-YL]GLYCYL}PYRROLIDINE-2-CARBONITRILE
4
NAG
19
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(17, 17)
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)
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 , HOH A:2006 , HOH A:2075 , HOH A:2211
BINDING SITE FOR RESIDUE LF7 A 801
02
AC2
SOFTWARE
GLY A:352 , TRP A:353 , ASN A:595 , ARG A:596 , ARG A:669 , GLY A:672 , NAG A:812 , HOH A:2327
BINDING SITE FOR RESIDUE GOL A 802
03
AC3
SOFTWARE
GLU A:73 , ASN A:74 , ASN A:75 , ASN A:92
BINDING SITE FOR RESIDUE NAG A 805
04
AC4
SOFTWARE
ARG A:147 , ILE A:148 , ASN A:150
BINDING SITE FOR RESIDUE NAG A 806
05
AC5
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , HOH A:2067
BINDING SITE FOR RESIDUE NAG A 809
06
AC6
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , TYR B:547 , SER B:630 , TYR B:631 , VAL B:656 , TYR B:662 , TYR B:666 , ASN B:710 , HOH B:954 , HOH B:973 , HOH B:1029
BINDING SITE FOR RESIDUE LF7 B 801
07
AC7
SOFTWARE
GLN B:320 , GLY B:352 , ASN B:595 , ARG B:596 , ARG B:669 , GLY B:672 , HOH B:1002
BINDING SITE FOR RESIDUE GOL B 802
08
AC8
SOFTWARE
ARG B:147 , ILE B:148 , ASN B:150
BINDING SITE FOR RESIDUE NAG B 805
09
AC9
SOFTWARE
VAL B:279 , ASN B:281
BINDING SITE FOR RESIDUE NAG B 810
10
BC1
SOFTWARE
VAL A:78 , TYR A:83 , ASN A:85 , SER A:86 , SER A:87 , HOH A:2131
BINDING SITE FOR LINKED RESIDUES A 803 to 804
11
BC2
SOFTWARE
ASN A:219 , THR A:221 , ASN A:272 , GLN A:308 , GLU A:309 , TYR A:330 , GLU A:332 , HOH A:2148 , HOH A:2399
BINDING SITE FOR LINKED RESIDUES A 807 to 808
12
BC3
SOFTWARE
TRP A:187 , THR A:188 , ASN A:281 , HOH A:2072 , HOH A:2169 , HOH A:2340 , HOH A:2348
BINDING SITE FOR LINKED RESIDUES A 810 to 811
13
BC4
SOFTWARE
ASN A:321 , MET A:348 , SER A:349 , THR A:350 , GOL A:802
BINDING SITE FOR LINKED RESIDUES A 812 to 813
14
BC5
SOFTWARE
ASN A:179 , GLU B:67 , ASN B:80 , ASN B:85 , SER B:86 , SER B:87 , HOH B:1056
BINDING SITE FOR LINKED RESIDUES B 803 to 804
15
BC6
SOFTWARE
ASN B:219 , THR B:221 , ASN B:272 , GLN B:308 , GLU B:309 , TYR B:330 , GLU B:332 , HOH B:1200
BINDING SITE FOR LINKED RESIDUES B 806 to 807
16
BC7
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , HOH B:1235 , HOH B:1258
BINDING SITE FOR LINKED RESIDUES B 808 to 809
17
BC8
SOFTWARE
ASN B:321 , SER B:349 , ARG B:596 , ASP B:678
BINDING SITE FOR LINKED RESIDUES B 811 to 812
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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 (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_HUMAN
605-635
2
A:605-635
B:605-635
[
close PROSITE info
]
Exons
(24, 48)
Info
All Exons
Exon 1.3a (A:38-65 | B:38-65)
Exon 1.4a (A:65-95 | B:65-95)
Exon 1.5 (A:96-122 | B:96-122)
Exon 1.6 (A:123-140 | B:123-140)
Exon 1.7b (A:140-164 | B:140-164)
Exon 1.8c (A:165-205 | B:165-205)
Exon 1.9 (A:205-258 | B:205-258)
Exon 1.10 (A:259-296 | B:259-296)
Exon 1.12 (A:296-341 | B:296-341)
Exon 1.13 (A:342-356 | B:342-356)
Exon 1.15 (A:357-392 | B:357-392)
Exon 1.16 (A:393-415 | B:393-415)
Exon 1.17 (A:415-433 | B:415-433)
Exon 1.18 (A:433-474 | B:433-474)
Exon 1.20 (A:474-490 | B:474-490)
Exon 1.21b (A:490-523 | B:490-523)
Exon 1.22a (A:523-546 | B:523-546)
Exon 1.23 (A:546-611 | B:546-611)
Exon 1.24 (A:611-629 | B:611-629)
Exon 1.25 (A:630-663 | B:630-663)
Exon 1.26a (A:663-684 | B:663-684)
Exon 1.27a (A:685-709 | B:685-709)
Exon 1.28 (A:709-733 | B:709-733)
Exon 1.29b (A:734-766 | B:734-766)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2b/1.3a
02: Boundary 1.3a/1.4a
03: Boundary 1.4a/1.5
04: Boundary 1.5/1.6
05: Boundary 1.6/1.7b
06: Boundary 1.7b/1.8c
07: Boundary 1.8c/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.12
10: Boundary 1.12/1.13
11: Boundary 1.13/1.15
12: Boundary 1.15/1.16
13: Boundary 1.16/1.17
14: Boundary 1.17/1.18
15: Boundary 1.18/1.20
16: Boundary 1.20/1.21b
17: Boundary 1.21b/1.22a
18: Boundary 1.22a/1.23
19: Boundary 1.23/1.24
20: Boundary 1.24/1.25
21: Boundary 1.25/1.26a
22: Boundary 1.26a/1.27a
23: Boundary 1.27a/1.28
24: Boundary 1.28/1.29b
25: Boundary 1.29b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000360534
1a
ENSE00001428031
chr2:
162931052-162930486
567
DPP4_HUMAN
1-2
2
0
-
-
1.2b
ENST00000360534
2b
ENSE00001405430
chr2:
162929996-162929909
88
DPP4_HUMAN
3-32
30
0
-
-
1.3a
ENST00000360534
3a
ENSE00001407496
chr2:
162904011-162903913
99
DPP4_HUMAN
32-65
34
2
A:38-65
B:38-65
28
28
1.4a
ENST00000360534
4a
ENSE00001401296
chr2:
162903516-162903425
92
DPP4_HUMAN
65-95
31
2
A:65-95
B:65-95
31
31
1.5
ENST00000360534
5
ENSE00001700120
chr2:
162902122-162902042
81
DPP4_HUMAN
96-122
27
2
A:96-122
B:96-122
27
27
1.6
ENST00000360534
6
ENSE00001731265
chr2:
162895694-162895642
53
DPP4_HUMAN
123-140
18
2
A:123-140
B:123-140
18
18
1.7b
ENST00000360534
7b
ENSE00001687658
chr2:
162895531-162895459
73
DPP4_HUMAN
140-164
25
2
A:140-164
B:140-164
25
25
1.8c
ENST00000360534
8c
ENSE00001752447
chr2:
162894932-162894812
121
DPP4_HUMAN
165-205
41
2
A:165-205
B:165-205
41
41
1.9
ENST00000360534
9
ENSE00001671980
chr2:
162891834-162891674
161
DPP4_HUMAN
205-258
54
2
A:205-258
B:205-258
54
54
1.10
ENST00000360534
10
ENSE00001629068
chr2:
162890163-162890051
113
DPP4_HUMAN
259-296
38
2
A:259-296
B:259-296
38
38
1.12
ENST00000360534
12
ENSE00001774486
chr2:
162881449-162881314
136
DPP4_HUMAN
296-341
46
2
A:296-341
B:296-341
46
46
1.13
ENST00000360534
13
ENSE00001608277
chr2:
162879309-162879265
45
DPP4_HUMAN
342-356
15
2
A:342-356
B:342-356
15
15
1.15
ENST00000360534
15
ENSE00001792529
chr2:
162877198-162877091
108
DPP4_HUMAN
357-392
36
2
A:357-392
B:357-392
36
36
1.16
ENST00000360534
16
ENSE00001609652
chr2:
162876806-162876739
68
DPP4_HUMAN
393-415
23
2
A:393-415
B:393-415
23
23
1.17
ENST00000360534
17
ENSE00001661516
chr2:
162875786-162875733
54
DPP4_HUMAN
415-433
19
2
A:415-433
B:415-433
19
19
1.18
ENST00000360534
18
ENSE00001734062
chr2:
162875360-162875239
122
DPP4_HUMAN
433-474
42
2
A:433-474
B:433-474
42
42
1.20
ENST00000360534
20
ENSE00001689663
chr2:
162873665-162873618
48
DPP4_HUMAN
474-490
17
2
A:474-490
B:474-490
17
17
1.21b
ENST00000360534
21b
ENSE00001601165
chr2:
162873376-162873278
99
DPP4_HUMAN
490-523
34
2
A:490-523
B:490-523
34
34
1.22a
ENST00000360534
22a
ENSE00001793185
chr2:
162870975-162870906
70
DPP4_HUMAN
523-546
24
2
A:523-546
B:523-546
24
24
1.23
ENST00000360534
23
ENSE00001624874
chr2:
162868497-162868303
195
DPP4_HUMAN
546-611
66
2
A:546-611
B:546-611
66
66
1.24
ENST00000360534
24
ENSE00001805530
chr2:
162865805-162865751
55
DPP4_HUMAN
611-629
19
2
A:611-629
B:611-629
19
19
1.25
ENST00000360534
25
ENSE00001766271
chr2:
162865171-162865072
100
DPP4_HUMAN
630-663
34
2
A:630-663
B:630-663
34
34
1.26a
ENST00000360534
26a
ENSE00001658910
chr2:
162862319-162862255
65
DPP4_HUMAN
663-684
22
2
A:663-684
B:663-684
22
22
1.27a
ENST00000360534
27a
ENSE00001776448
chr2:
162851882-162851810
73
DPP4_HUMAN
685-709
25
2
A:685-709
B:685-709
25
25
1.28
ENST00000360534
28
ENSE00001768665
chr2:
162851544-162851471
74
DPP4_HUMAN
709-733
25
2
A:709-733
B:709-733
25
25
1.29b
ENST00000360534
29b
ENSE00001420909
chr2:
162849894-162848751
1144
DPP4_HUMAN
734-766
33
2
A:734-766
B:734-766
33
33
[
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3w2ta1 (A:38-508)
1b: SCOP_d3w2tb1 (B:38-508)
2a: SCOP_d3w2ta2 (A:509-766)
2b: SCOP_d3w2tb2 (B:509-766)
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Protein Domains
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(
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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)
Human (Homo sapiens) [TaxId: 9606]
(80)
1a
d3w2ta1
A:38-508
1b
d3w2tb1
B:38-508
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)
Human (Homo sapiens) [TaxId: 9606]
(54)
2a
d3w2ta2
A:509-766
2b
d3w2tb2
B:509-766
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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all PFAM domains
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Sorry, no Info available
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