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1R9M
Biol. Unit 2
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
[
close entry info
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Hetero Components
(2, 17)
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
2
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: CC7 (SOFTWARE)
02: CC8 (SOFTWARE)
03: CC9 (SOFTWARE)
04: DC1 (SOFTWARE)
05: DC2 (SOFTWARE)
06: DC3 (SOFTWARE)
07: DC4 (SOFTWARE)
08: DC5 (SOFTWARE)
09: DC6 (SOFTWARE)
10: DC7 (SOFTWARE)
11: DC8 (SOFTWARE)
12: DC9 (SOFTWARE)
13: EC1 (SOFTWARE)
14: EC2 (SOFTWARE)
15: EC3 (SOFTWARE)
16: EC4 (SOFTWARE)
17: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC7
SOFTWARE
ILE C:148 , ASN C:150
BINDING SITE FOR RESIDUE NAG C 1501
02
CC8
SOFTWARE
ASN C:219 , GLN C:308 , GLU C:309
BINDING SITE FOR RESIDUE NAG C 2191
03
CC9
SOFTWARE
ASN C:229 , THR C:231 , GLU C:232 , NAG C:2292 , HOH C:5476 , HOH C:5527
BINDING SITE FOR RESIDUE NAG C 2291
04
DC1
SOFTWARE
NAG C:2291 , MAN C:2293 , HOH C:5527
BINDING SITE FOR RESIDUE NAG C 2292
05
DC2
SOFTWARE
NAG C:2292 , MAN C:2294
BINDING SITE FOR RESIDUE MAN C 2293
06
DC3
SOFTWARE
MAN C:2293 , HOH C:5413
BINDING SITE FOR RESIDUE MAN C 2294
07
DC4
SOFTWARE
TRP C:187 , ASN C:281
BINDING SITE FOR RESIDUE NAG C 2811
08
DC5
SOFTWARE
ASN C:321 , HOH C:5415
BINDING SITE FOR RESIDUE NAG C 3211
09
DC6
SOFTWARE
LEU C:519 , ASN C:520 , ARG C:581 , ASP C:605
BINDING SITE FOR RESIDUE NAG C 5201
10
DC7
SOFTWARE
ARG D:147 , ILE D:148 , ASN D:150
BINDING SITE FOR RESIDUE NAG D 1501
11
DC8
SOFTWARE
ASN D:219 , THR D:221 , GLN D:308 , GLU D:309 , HOH D:7147
BINDING SITE FOR RESIDUE NAG D 2191
12
DC9
SOFTWARE
ASN D:229 , THR D:231 , GLU D:232 , NAG D:2292 , HOH D:6980
BINDING SITE FOR RESIDUE NAG D 2291
13
EC1
SOFTWARE
NAG D:2291
BINDING SITE FOR RESIDUE NAG D 2292
14
EC2
SOFTWARE
TRP D:187 , VAL D:279 , ASN D:281 , HOH D:7142
BINDING SITE FOR RESIDUE NAG D 2811
15
EC3
SOFTWARE
ILE D:319 , ASN D:321 , ARG D:596 , HOH D:6972 , HOH D:7216
BINDING SITE FOR RESIDUE NAG D 3211
16
EC4
SOFTWARE
ASN D:520 , PHE D:524 , ARG D:581 , ASP D:605 , HOH D:6960
BINDING SITE FOR RESIDUE NAG D 5201
17
EC5
SOFTWARE
ASP D:681 , ASN D:685
BINDING SITE FOR RESIDUE NAG D 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 (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_HUMAN
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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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
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)
(
)
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)
View:
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Clans
(
)
(
)
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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Asymmetric Unit 1
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Asym.Unit (526 KB)
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