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1R9M
Biol. Unit 1
Info
Asym.Unit (526 KB)
Biol.Unit 1 (263 KB)
Biol.Unit 2 (256 KB)
Biol.Unit 3 (512 KB)
Biol.Unit 4 (512 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DIPEPTIDYL PEPTIDASE IV AT 2.1 ANG. RESOLUTION.
Authors
:
K. Aertgeerts, S. Ye, M. G. Tennant, B. Collins, J. Rogers, B. C. Sang, R. D. R. Webb, G. S. Prasad
Date
:
30 Oct 03 (Deposition) - 29 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
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
:
Aminopeptidase, Serine Protease, Glycoprotein, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Aertgeerts, S. Ye, M. G. Tennant, M. L. Kraus, J. Rogers, B. C. Sang, R. J. Skene, D. R. Webb, G. S. Prasad
Crystal Structure Of Human Dipeptidyl Peptidase Iv In Complex With A Decapeptide Reveals Details On Substrate Specificity And Tetrahedral Intermediate Formation.
Protein Sci. V. 13 412 2004
[
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
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)
3ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
3ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
3aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
3ak: N-ACETYL-D-GLUCOSAMINE (NAGak)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
2
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
22
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:83 , ASN A:85 , SER A:86 , SER A:87 , HOH A:7265
BINDING SITE FOR RESIDUE NAG A 851
02
AC2
SOFTWARE
ASN A:150 , NAG A:1502 , HOH A:6971 , HOH A:7190
BINDING SITE FOR RESIDUE NAG A 1501
03
AC3
SOFTWARE
NAG A:1501 , HOH A:7299
BINDING SITE FOR RESIDUE NAG A 1502
04
AC4
SOFTWARE
ASN A:219 , THR A:221 , GLN A:308 , GLU A:309 , HOH A:6978
BINDING SITE FOR RESIDUE NAG A 2191
05
AC5
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , NAG A:2292 , HOH A:6980
BINDING SITE FOR RESIDUE NAG A 2291
06
AC6
SOFTWARE
NAG A:2291 , MAN A:2293 , HOH A:7174 , HOH A:7317
BINDING SITE FOR RESIDUE NAG A 2292
07
AC7
SOFTWARE
NAG A:2292
BINDING SITE FOR RESIDUE MAN A 2293
08
AC8
SOFTWARE
TRP A:187 , ASN A:281 , NAG A:2812 , HOH A:7213
BINDING SITE FOR RESIDUE NAG A 2811
09
AC9
SOFTWARE
NAG A:2811
BINDING SITE FOR RESIDUE NAG A 2812
10
BC1
SOFTWARE
ASN A:321 , SER A:349 , THR A:350 , ARG A:596 , NAG A:3212 , HOH A:6900
BINDING SITE FOR RESIDUE NAG A 3211
11
BC2
SOFTWARE
NAG A:3211
BINDING SITE FOR RESIDUE NAG A 3212
12
BC3
SOFTWARE
ASN A:520 , PHE A:524 , ARG A:581 , ASP A:605
BINDING SITE FOR RESIDUE NAG A 5201
13
BC4
SOFTWARE
ASP A:681 , ARG A:684 , ASN A:685
BINDING SITE FOR RESIDUE NAG A 6851
14
BC5
SOFTWARE
VAL B:78 , ASN B:85 , SER B:87 , HOH B:7012
BINDING SITE FOR RESIDUE NAG B 851
15
BC6
SOFTWARE
ARG B:147 , ILE B:148 , ASN B:150 , FUC B:1502
BINDING SITE FOR RESIDUE NAG B 1501
16
BC7
SOFTWARE
NAG B:1501
BINDING SITE FOR RESIDUE FUC B 1502
17
BC8
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309 , NAG B:2192
BINDING SITE FOR RESIDUE NAG B 2191
18
BC9
SOFTWARE
ASN B:272 , GLU B:332 , NAG B:2191
BINDING SITE FOR RESIDUE NAG B 2192
19
CC1
SOFTWARE
ASN B:229 , THR B:231 , GLU B:232 , NAG B:2292 , HOH B:7211
BINDING SITE FOR RESIDUE NAG B 2291
20
CC2
SOFTWARE
GLU B:232 , NAG B:2291
BINDING SITE FOR RESIDUE NAG B 2292
21
CC3
SOFTWARE
ASN B:281 , HOH B:6898 , HOH B:7133
BINDING SITE FOR RESIDUE NAG B 2811
22
CC4
SOFTWARE
ASN B:321 , SER B:349 , THR B:350 , HOH B:7237
BINDING SITE FOR RESIDUE NAG B 3211
23
CC5
SOFTWARE
LEU B:519 , ASN B:520 , PHE B:524 , ARG B:581 , HOH B:7200
BINDING SITE FOR RESIDUE NAG B 5201
24
CC6
SOFTWARE
ASP B:681 , ARG B:684 , ASN B:685 , HOH B:7011
BINDING SITE FOR RESIDUE NAG B 6851
[
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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 (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
-
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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_d1r9ma1 (A:40-508)
1b: SCOP_d1r9mb1 (B:40-508)
1c: SCOP_d1r9mc1 (C:40-508)
1d: SCOP_d1r9md1 (D:40-508)
2a: SCOP_d1r9ma2 (A:509-766)
2b: SCOP_d1r9mb2 (B:509-766)
2c: SCOP_d1r9mc2 (C:509-766)
2d: SCOP_d1r9md2 (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)
Human (Homo sapiens) [TaxId: 9606]
(80)
1a
d1r9ma1
A:40-508
1b
d1r9mb1
B:40-508
1c
d1r9mc1
C:40-508
1d
d1r9md1
D:40-508
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
d1r9ma2
A:509-766
2b
d1r9mb2
B:509-766
2c
d1r9mc2
C:509-766
2d
d1r9md2
D:509-766
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1r9mA02 (A:509-766)
1b: CATH_1r9mB02 (B:509-766)
1c: CATH_1r9mC02 (C:509-766)
1d: CATH_1r9mD02 (D:509-766)
2a: CATH_1r9mB01 (B:39-508)
2b: CATH_1r9mA01 (A:40-508)
2c: CATH_1r9mC01 (C:40-508)
2d: CATH_1r9mD01 (D:40-508)
View:
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(
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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)
Human (Homo sapiens)
(118)
1a
1r9mA02
A:509-766
1b
1r9mB02
B:509-766
1c
1r9mC02
C:509-766
1d
1r9mD02
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)
Human (Homo sapiens)
(59)
2a
1r9mB01
B:39-508
2b
1r9mA01
A:40-508
2c
1r9mC01
C:40-508
2d
1r9mD01
D:40-508
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_1r9mD01 (D:559-765)
1b: PFAM_Peptidase_S9_1r9mD02 (D:559-765)
1c: PFAM_Peptidase_S9_1r9mD03 (D:559-765)
1d: PFAM_Peptidase_S9_1r9mD04 (D:559-765)
2a: PFAM_DPPIV_N_1r9mD05 (D:108-479)
2b: PFAM_DPPIV_N_1r9mD06 (D:108-479)
2c: PFAM_DPPIV_N_1r9mD07 (D:108-479)
2d: PFAM_DPPIV_N_1r9mD08 (D:108-479)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Homo sapiens (Human)
(33)
1a
Peptidase_S9-1r9mD01
D:559-765
1b
Peptidase_S9-1r9mD02
D:559-765
1c
Peptidase_S9-1r9mD03
D:559-765
1d
Peptidase_S9-1r9mD04
D:559-765
Clan
:
Beta_propeller
(192)
Family
:
DPPIV_N
(38)
Homo sapiens (Human)
(33)
2a
DPPIV_N-1r9mD05
D:108-479
2b
DPPIV_N-1r9mD06
D:108-479
2c
DPPIV_N-1r9mD07
D:108-479
2d
DPPIV_N-1r9mD08
D:108-479
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Asym.Unit (526 KB)
Header - Asym.Unit
Biol.Unit 1 (263 KB)
Header - Biol.Unit 1
Biol.Unit 2 (256 KB)
Header - Biol.Unit 2
Biol.Unit 3 (512 KB)
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