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1W1I
Biol. Unit 1
Info
Asym.Unit (731 KB)
Biol.Unit 1 (363 KB)
Biol.Unit 2 (363 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIPEPTIDYL PEPTIDASE IV (DPPIV OR CD26) IN COMPLEX WITH ADENOSINE DEAMINASE
Authors
:
W. A. Weihofen, J. Liu, W. Reutter, W. Saenger, H. Fan
Date
:
22 Jun 04 (Deposition) - 02 Sep 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.03
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)
Keywords
:
Hydrolase, Hydrolase/Complex, Dipetidyl Peptidase Iv, Dppiv, Cd26, Alpha/Beta-Hydrolase Fold, Beta-Propeller Fold, Protein-Protein Complex, Adenosine Deaminase, Ada, Serine Protease, Aminopeptidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. A. Weihofen, J. Liu, W. Reutter, W. Saenger, H. Fan
Crystal Structure Of Cd26/Dipeptidyl-Peptidase Iv In Complex With Adenosine Deaminase Reveals A Highly Amphiphilic Interface
J. Biol. Chem. V. 279 43330 2004
[
close entry info
]
Hetero Components
(5, 29)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
2c: ALPHA-L-FUCOSE (FUCc)
2d: ALPHA-L-FUCOSE (FUCd)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
4ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
4ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
4ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
4ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
4af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
4ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
4ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
4ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
4aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
4ak: N-ACETYL-D-GLUCOSAMINE (NAGak)
4al: N-ACETYL-D-GLUCOSAMINE (NAGal)
4am: N-ACETYL-D-GLUCOSAMINE (NAGam)
4an: N-ACETYL-D-GLUCOSAMINE (NAGan)
4ao: N-ACETYL-D-GLUCOSAMINE (NAGao)
4ap: N-ACETYL-D-GLUCOSAMINE (NAGap)
4aq: N-ACETYL-D-GLUCOSAMINE (NAGaq)
4ar: N-ACETYL-D-GLUCOSAMINE (NAGar)
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)
4t: N-ACETYL-D-GLUCOSAMINE (NAGt)
4u: N-ACETYL-D-GLUCOSAMINE (NAGu)
4v: N-ACETYL-D-GLUCOSAMINE (NAGv)
4w: N-ACETYL-D-GLUCOSAMINE (NAGw)
4x: N-ACETYL-D-GLUCOSAMINE (NAGx)
4y: N-ACETYL-D-GLUCOSAMINE (NAGy)
4z: N-ACETYL-D-GLUCOSAMINE (NAGz)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
5c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
3
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
20
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
3
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(32, 32)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: EC8 (SOFTWARE)
28: GC3 (SOFTWARE)
29: GC4 (SOFTWARE)
30: GC5 (SOFTWARE)
31: GC6 (SOFTWARE)
32: GC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:85 , SER A:86 , SER A:87 , NAG A:801 , FUC A:802
BINDING SITE FOR RESIDUE NAG A 800
02
AC2
SOFTWARE
NAG A:800 , FUC A:802
BINDING SITE FOR RESIDUE NAG A 801
03
AC3
SOFTWARE
NAG A:800 , NAG A:801
BINDING SITE FOR RESIDUE FUC A 802
04
AC4
SOFTWARE
ARG A:147 , ASN A:150 , NAG A:811
BINDING SITE FOR RESIDUE NAG A 810
05
AC5
SOFTWARE
NAG A:810
BINDING SITE FOR RESIDUE NAG A 811
06
AC6
SOFTWARE
ASN A:219 , THR A:221 , GLU A:309 , NAG A:821
BINDING SITE FOR RESIDUE NAG A 820
07
AC7
SOFTWARE
THR A:221 , ASN A:272 , GLU A:332 , NAG A:820
BINDING SITE FOR RESIDUE NAG A 821
08
AC8
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , NAG A:831
BINDING SITE FOR RESIDUE NAG A 830
09
AC9
SOFTWARE
THR A:231 , NAG A:830 , BMA A:832 , ARG F:33 , ARG F:34 , GLY F:35
BINDING SITE FOR RESIDUE NAG A 831
10
BC1
SOFTWARE
NAG A:831 , MAN A:833 , ARG F:34 , GLY F:35
BINDING SITE FOR RESIDUE BMA A 832
11
BC2
SOFTWARE
BMA A:832 , GLY F:35
BINDING SITE FOR RESIDUE MAN A 833
12
BC3
SOFTWARE
VAL A:279 , ASN A:281
BINDING SITE FOR RESIDUE NAG A 840
13
BC4
SOFTWARE
ASN A:321 , SER A:349 , ARG A:596
BINDING SITE FOR RESIDUE NAG A 850
14
BC5
SOFTWARE
ASN B:85 , SER B:87 , FUC B:802
BINDING SITE FOR RESIDUE NAG B 800
15
BC6
SOFTWARE
TYR B:83 , NAG B:800 , SER C:412 , ASP C:413
BINDING SITE FOR RESIDUE FUC B 802
16
BC7
SOFTWARE
ARG B:147 , ASN B:150
BINDING SITE FOR RESIDUE NAG B 810
17
BC8
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309 , NAG B:821
BINDING SITE FOR RESIDUE NAG B 820
18
BC9
SOFTWARE
THR B:221 , GLU B:332 , NAG B:820
BINDING SITE FOR RESIDUE NAG B 821
19
CC1
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , NAG B:831 , ARG E:33
BINDING SITE FOR RESIDUE NAG B 830
20
CC2
SOFTWARE
THR B:231 , NAG B:830 , BMA B:832 , ARG E:33 , ARG E:34 , GLY E:35
BINDING SITE FOR RESIDUE NAG B 831
21
CC3
SOFTWARE
NAG B:831 , MAN B:833 , GLY E:35
BINDING SITE FOR RESIDUE BMA B 832
22
CC4
SOFTWARE
BMA B:832 , GLY E:35 , ILE E:36
BINDING SITE FOR RESIDUE MAN B 833
23
CC5
SOFTWARE
ASN A:450 , TRP B:187 , ASN B:281
BINDING SITE FOR RESIDUE NAG B 840
24
CC6
SOFTWARE
ASN B:321 , NAG B:851
BINDING SITE FOR RESIDUE NAG B 850
25
CC7
SOFTWARE
NAG B:850
BINDING SITE FOR RESIDUE NAG B 851
26
CC8
SOFTWARE
GLU B:73 , ASN B:74 , ASN B:75 , ASN B:92 , ARG F:352
BINDING SITE FOR RESIDUE NAG B 870
27
EC8
SOFTWARE
GLU B:521 , ASN D:85 , NAG D:800
BINDING SITE FOR RESIDUE FUC D 802
28
GC3
SOFTWARE
ASN A:520 , ARG A:581
BINDING SITE FOR RESIDUE NDG A 860
29
GC4
SOFTWARE
GLU A:73 , ASN A:75 , ASN A:92
BINDING SITE FOR RESIDUE NDG A 870
30
GC5
SOFTWARE
ASN B:520
BINDING SITE FOR RESIDUE NDG B 860
31
GC6
SOFTWARE
HIS E:15 , HIS E:17 , HIS E:214 , ASP E:295
BINDING SITE FOR RESIDUE ZN E 501
32
GC7
SOFTWARE
HIS F:15 , HIS F:17 , HIS F:214 , ASP F:295
BINDING SITE FOR RESIDUE ZN F 501
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_ADA_BOVIN_001 (Q199Q, chain E/F, )
2: VAR_ADA_BOVIN_002 (T246T, chain E/F, )
3: VAR_ADA_BOVIN_003 (R352R, chain E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_ADA_BOVIN_001
*
K
199
Q
ADA_BOVIN
---
---
E/F
Q
199
Q
2
UniProt
VAR_ADA_BOVIN_002
*
A
246
T
ADA_BOVIN
---
---
E/F
T
246
T
3
UniProt
VAR_ADA_BOVIN_003
*
G
352
R
ADA_BOVIN
---
---
E/F
R
352
R
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: A_DEAMINASE (E:291-297,F:291-297)
2: 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
A_DEAMINASE
PS00485
Adenosine and AMP deaminase signature.
ADA_BOVIN
291-297
2
E:291-297
F:291-297
-
-
2
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
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1w1ia1 (A:39-508)
1b: SCOP_d1w1ib1 (B:39-508)
1c: SCOP_d1w1ic1 (C:39-508)
1d: SCOP_d1w1id1 (D:39-508)
2a: SCOP_d1w1ia2 (A:509-766)
2b: SCOP_d1w1ib2 (B:509-766)
2c: SCOP_d1w1ic2 (C:509-766)
2d: SCOP_d1w1id2 (D:509-766)
3a: SCOP_d1w1ie_ (E:)
3b: SCOP_d1w1if_ (F:)
3c: SCOP_d1w1ig_ (G:)
3d: SCOP_d1w1ih_ (H:)
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
d1w1ia1
A:39-508
1b
d1w1ib1
B:39-508
1c
d1w1ic1
C:39-508
1d
d1w1id1
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)
Human (Homo sapiens) [TaxId: 9606]
(54)
2a
d1w1ia2
A:509-766
2b
d1w1ib2
B:509-766
2c
d1w1ic2
C:509-766
2d
d1w1id2
D:509-766
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Adenosine/AMP deaminase
(36)
Protein domain
:
Adenosine deaminase (ADA)
(24)
Cow (Bos taurus) [TaxId: 9913]
(12)
3a
d1w1ie_
E:
3b
d1w1if_
F:
3c
d1w1ig_
G:
3d
d1w1ih_
H:
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1w1iA02 (A:509-766)
1b: CATH_1w1iB02 (B:509-766)
1c: CATH_1w1iC02 (C:509-766)
1d: CATH_1w1iD02 (D:509-766)
2a: CATH_1w1iE00 (E:4-355)
2b: CATH_1w1iF00 (F:4-355)
2c: CATH_1w1iG00 (G:4-355)
2d: CATH_1w1iH00 (H:4-355)
3a: CATH_1w1iA01 (A:39-508)
3b: CATH_1w1iB01 (B:39-508)
3c: CATH_1w1iC01 (C:39-508)
3d: CATH_1w1iD01 (D:39-508)
View:
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Classes
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)
(
)
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)
Human (Homo sapiens)
(118)
1a
1w1iA02
A:509-766
1b
1w1iB02
B:509-766
1c
1w1iC02
C:509-766
1d
1w1iD02
D:509-766
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Human (Homo sapiens)
(5)
2a
1w1iE00
E:4-355
2b
1w1iF00
F:4-355
2c
1w1iG00
G:4-355
2d
1w1iH00
H:4-355
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)
3a
1w1iA01
A:39-508
3b
1w1iB01
B:39-508
3c
1w1iC01
C:39-508
3d
1w1iD01
D:39-508
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_1w1iD01 (D:559-765)
1b: PFAM_Peptidase_S9_1w1iD02 (D:559-765)
1c: PFAM_Peptidase_S9_1w1iD03 (D:559-765)
1d: PFAM_Peptidase_S9_1w1iD04 (D:559-765)
2a: PFAM_A_deaminase_1w1iH01 (H:8-346)
2b: PFAM_A_deaminase_1w1iH02 (H:8-346)
2c: PFAM_A_deaminase_1w1iH03 (H:8-346)
2d: PFAM_A_deaminase_1w1iH04 (H:8-346)
3a: PFAM_DPPIV_N_1w1iD05 (D:108-479)
3b: PFAM_DPPIV_N_1w1iD06 (D:108-479)
3c: PFAM_DPPIV_N_1w1iD07 (D:108-479)
3d: PFAM_DPPIV_N_1w1iD08 (D:108-479)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Homo sapiens (Human)
(33)
1a
Peptidase_S9-1w1iD01
D:559-765
1b
Peptidase_S9-1w1iD02
D:559-765
1c
Peptidase_S9-1w1iD03
D:559-765
1d
Peptidase_S9-1w1iD04
D:559-765
Clan
:
Amidohydrolase
(126)
Family
:
A_deaminase
(23)
Bos taurus (Bovine)
(14)
2a
A_deaminase-1w1iH01
H:8-346
2b
A_deaminase-1w1iH02
H:8-346
2c
A_deaminase-1w1iH03
H:8-346
2d
A_deaminase-1w1iH04
H:8-346
Clan
:
Beta_propeller
(192)
Family
:
DPPIV_N
(38)
Homo sapiens (Human)
(33)
3a
DPPIV_N-1w1iD05
D:108-479
3b
DPPIV_N-1w1iD06
D:108-479
3c
DPPIV_N-1w1iD07
D:108-479
3d
DPPIV_N-1w1iD08
D:108-479
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain E
Chain F
Asymmetric Unit 1
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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