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1R9N
Biol. Unit 1
Info
Asym.Unit (520 KB)
Biol.Unit 1 (261 KB)
Biol.Unit 2 (255 KB)
Biol.Unit 3 (255 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DIPEPTIDYL PEPTIDASE IV IN COMPLEX WITH A DECAPEPTIDE (TNPY) AT 2.3 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 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,E,F (1x)
Biol. Unit 2: C,D,G,H (1x)
Biol. Unit 3: C,D,G,H (1x)
Keywords
:
Alpha/Beta Hydrolase, Eight-Bladed Beta Propeller, Serine Protease, 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
(1, 15)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
1q: N-ACETYL-D-GLUCOSAMINE (NAGq)
1r: N-ACETYL-D-GLUCOSAMINE (NAGr)
1s: N-ACETYL-D-GLUCOSAMINE (NAGs)
1t: N-ACETYL-D-GLUCOSAMINE (NAGt)
1u: N-ACETYL-D-GLUCOSAMINE (NAGu)
1v: N-ACETYL-D-GLUCOSAMINE (NAGv)
1w: N-ACETYL-D-GLUCOSAMINE (NAGw)
1x: N-ACETYL-D-GLUCOSAMINE (NAGx)
1y: N-ACETYL-D-GLUCOSAMINE (NAGy)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(15, 15)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:78 , ASN A:85 , SER A:86 , SER A:87
BINDING SITE FOR RESIDUE NAG A 851
02
AC2
SOFTWARE
ARG A:147 , ASN A:150
BINDING SITE FOR RESIDUE NAG A 1501
03
AC3
SOFTWARE
ASN A:219 , THR A:221 , GLN A:308 , GLU A:309
BINDING SITE FOR RESIDUE NAG A 2191
04
AC4
SOFTWARE
ASN A:229 , THR A:231 , GLU A:232 , NAG A:2292
BINDING SITE FOR RESIDUE NAG A 2291
05
AC5
SOFTWARE
THR A:231 , NAG A:2291
BINDING SITE FOR RESIDUE NAG A 2292
06
AC6
SOFTWARE
TRP A:187 , ASN A:281 , HOH A:6880
BINDING SITE FOR RESIDUE NAG A 2811
07
AC7
SOFTWARE
ILE A:319 , ASN A:321 , SER A:349
BINDING SITE FOR RESIDUE NAG A 3211
08
AC8
SOFTWARE
ASP A:681 , ARG A:684 , ASN A:685
BINDING SITE FOR RESIDUE NAG A 6851
09
AC9
SOFTWARE
ASN B:85 , SER B:86 , SER B:87 , HOH B:3377 , HOH B:3378 , HOH B:3402
BINDING SITE FOR RESIDUE NAG B 851
10
BC1
SOFTWARE
ASN B:150
BINDING SITE FOR RESIDUE NAG B 1501
11
BC2
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309 , HOH B:3394
BINDING SITE FOR RESIDUE NAG B 2191
12
BC3
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , NAG B:2292
BINDING SITE FOR RESIDUE NAG B 2291
13
BC4
SOFTWARE
GLU B:232 , NAG B:2291
BINDING SITE FOR RESIDUE NAG B 2292
14
BC5
SOFTWARE
TRP B:187 , ASN B:281 , HOH B:3247
BINDING SITE FOR RESIDUE NAG B 2811
15
BC6
SOFTWARE
ILE B:319 , ASN B:321 , SER B:349
BINDING SITE FOR RESIDUE NAG B 3211
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PANCREATIC_HORMONE_2 (E:1001-1004,F:1001-1006)
2: PRO_ENDOPEP_SER (A:605-635,B:605-635)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PANCREATIC_HORMONE_2
PS50276
Pancreatic hormone family profile.
NPY_MACMU
29-64
2
E:1001-1004
F:1001-1006
-
-
2
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
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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_d1r9na1 (A:39-508)
1b: SCOP_d1r9nb1 (B:39-508)
1c: SCOP_d1r9nc1 (C:40-508)
1d: SCOP_d1r9nd1 (D:40-508)
2a: SCOP_d1r9na2 (A:509-766)
2b: SCOP_d1r9nb2 (B:509-766)
2c: SCOP_d1r9nc2 (C:509-766)
2d: SCOP_d1r9nd2 (D:509-766)
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(
)
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)
(
)
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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)
Human (Homo sapiens) [TaxId: 9606]
(80)
1a
d1r9na1
A:39-508
1b
d1r9nb1
B:39-508
1c
d1r9nc1
C:40-508
1d
d1r9nd1
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
d1r9na2
A:509-766
2b
d1r9nb2
B:509-766
2c
d1r9nc2
C:509-766
2d
d1r9nd2
D:509-766
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1r9nA02 (A:509-766)
1b: CATH_1r9nB02 (B:509-766)
1c: CATH_1r9nC02 (C:509-766)
1d: CATH_1r9nD02 (D:509-766)
2a: CATH_1r9nC01 (C:40-508)
2b: CATH_1r9nD01 (D:40-508)
2c: CATH_1r9nA01 (A:39-508)
2d: CATH_1r9nB01 (B:36-508)
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Architectures
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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
1r9nA02
A:509-766
1b
1r9nB02
B:509-766
1c
1r9nC02
C:509-766
1d
1r9nD02
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
1r9nC01
C:40-508
2b
1r9nD01
D:40-508
2c
1r9nA01
A:39-508
2d
1r9nB01
B:36-508
[
close CATH info
]
Pfam Domains
(3, 10)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_1r9nD01 (D:559-765)
1b: PFAM_Peptidase_S9_1r9nD02 (D:559-765)
1c: PFAM_Peptidase_S9_1r9nD03 (D:559-765)
1d: PFAM_Peptidase_S9_1r9nD04 (D:559-765)
2a: PFAM_DPPIV_N_1r9nD05 (D:108-479)
2b: PFAM_DPPIV_N_1r9nD06 (D:108-479)
2c: PFAM_DPPIV_N_1r9nD07 (D:108-479)
2d: PFAM_DPPIV_N_1r9nD08 (D:108-479)
3a: PFAM_Hormone_3_1r9nH01 (H:1001-1005)
3b: PFAM_Hormone_3_1r9nH02 (H:1001-1005)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Homo sapiens (Human)
(33)
1a
Peptidase_S9-1r9nD01
D:559-765
1b
Peptidase_S9-1r9nD02
D:559-765
1c
Peptidase_S9-1r9nD03
D:559-765
1d
Peptidase_S9-1r9nD04
D:559-765
Clan
:
Beta_propeller
(192)
Family
:
DPPIV_N
(38)
Homo sapiens (Human)
(33)
2a
DPPIV_N-1r9nD05
D:108-479
2b
DPPIV_N-1r9nD06
D:108-479
2c
DPPIV_N-1r9nD07
D:108-479
2d
DPPIV_N-1r9nD08
D:108-479
Clan
:
no clan defined [family: Hormone_3]
(12)
Family
:
Hormone_3
(12)
Macaca mulatta (Rhesus macaque)
(1)
3a
Hormone_3-1r9nH01
H:1001-1005
3b
Hormone_3-1r9nH02
H:1001-1005
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Asym.Unit (520 KB)
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Biol.Unit 1 (261 KB)
Header - Biol.Unit 1
Biol.Unit 2 (255 KB)
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