PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2BGN
Biol. Unit 2
Info
Asym.Unit (738 KB)
Biol.Unit 1 (366 KB)
Biol.Unit 2 (366 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE TRP2-TAT (1-9) BOUND TO THE ACTIVE SITE OF DIPEPTIDYL PEPTIDASE IV (CD26)
Authors
:
W. A. Weihofen, J. Liu, W. Reutter, W. Saenger, H. Fan
Date
:
03 Jan 05 (Deposition) - 27 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.15
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,W,X,Y,Z
Biol. Unit 1: A,B,E,F,W,X (1x)
Biol. Unit 2: C,D,G,H,Y,Z (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, Hiv-1 Tat Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. A. Weihofen, J. Liu, W. Reutter, W. Saenger, H. Fan
Crystal Structures Of Hiv-1 Tat-Derived Nonapeptides Tat-(1-9) And Trp2-Tat-(1-9) Bound To The Active Site Of Dipeptidyl-Peptidase Iv (Cd26)
J. Biol. Chem. V. 280 14911 2005
[
close entry info
]
Hetero Components
(4, 30)
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: BETA-L-FUCOSE (FULa)
2b: BETA-L-FUCOSE (FULb)
2c: BETA-L-FUCOSE (FULc)
2d: BETA-L-FUCOSE (FULd)
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)
4as: N-ACETYL-D-GLUCOSAMINE (NAGas)
4at: N-ACETYL-D-GLUCOSAMINE (NAGat)
4au: N-ACETYL-D-GLUCOSAMINE (NAGau)
4av: N-ACETYL-D-GLUCOSAMINE (NAGav)
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: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
FUL
2
Ligand/Ion
BETA-L-FUCOSE
3
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
24
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(32, 32)
Info
All Sites
01: DC4 (SOFTWARE)
02: DC5 (SOFTWARE)
03: DC6 (SOFTWARE)
04: DC7 (SOFTWARE)
05: DC8 (SOFTWARE)
06: DC9 (SOFTWARE)
07: EC1 (SOFTWARE)
08: EC2 (SOFTWARE)
09: EC3 (SOFTWARE)
10: EC4 (SOFTWARE)
11: EC5 (SOFTWARE)
12: EC6 (SOFTWARE)
13: EC7 (SOFTWARE)
14: EC8 (SOFTWARE)
15: EC9 (SOFTWARE)
16: FC1 (SOFTWARE)
17: FC2 (SOFTWARE)
18: FC3 (SOFTWARE)
19: FC4 (SOFTWARE)
20: FC5 (SOFTWARE)
21: FC6 (SOFTWARE)
22: FC7 (SOFTWARE)
23: FC8 (SOFTWARE)
24: FC9 (SOFTWARE)
25: GC1 (SOFTWARE)
26: GC2 (SOFTWARE)
27: GC3 (SOFTWARE)
28: GC4 (SOFTWARE)
29: GC5 (SOFTWARE)
30: GC6 (SOFTWARE)
31: GC9 (SOFTWARE)
32: HC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
DC4
SOFTWARE
GLU C:67 , ASN C:85 , SER C:86 , SER C:87 , NAG C:801 , FUL C:802
BINDING SITE FOR RESIDUE NAG C 800
02
DC5
SOFTWARE
NAG C:800
BINDING SITE FOR RESIDUE NAG C 801
03
DC6
SOFTWARE
TYR C:83 , NAG C:800
BINDING SITE FOR RESIDUE FUL C 802
04
DC7
SOFTWARE
ARG C:147 , ILE C:148 , ASN C:150 , NAG C:811
BINDING SITE FOR RESIDUE NAG C 810
05
DC8
SOFTWARE
ARG C:147 , NAG C:810
BINDING SITE FOR RESIDUE NAG C 811
06
DC9
SOFTWARE
ASN C:219 , THR C:221 , GLN C:308 , GLU C:309 , NAG C:821
BINDING SITE FOR RESIDUE NAG C 820
07
EC1
SOFTWARE
GLU C:332 , NAG C:820
BINDING SITE FOR RESIDUE NAG C 821
08
EC2
SOFTWARE
ILE C:194 , ASN C:229 , THR C:231 , GLU C:232 , NAG C:831 , ARG G:33
BINDING SITE FOR RESIDUE NAG C 830
09
EC3
SOFTWARE
THR C:231 , NAG C:830 , BMA C:832 , ARG G:33 , ARG G:34 , GLY G:35
BINDING SITE FOR RESIDUE NAG C 831
10
EC4
SOFTWARE
NAG C:831 , MAN C:833 , GLY G:35
BINDING SITE FOR RESIDUE BMA C 832
11
EC5
SOFTWARE
BMA C:832 , ILE G:36
BINDING SITE FOR RESIDUE MAN C 833
12
EC6
SOFTWARE
TRP C:187 , ASN C:281
BINDING SITE FOR RESIDUE NAG C 840
13
EC7
SOFTWARE
ASN C:321 , MET C:348 , SER C:349 , NAG C:851
BINDING SITE FOR RESIDUE NAG C 850
14
EC8
SOFTWARE
NAG C:850
BINDING SITE FOR RESIDUE NAG C 851
15
EC9
SOFTWARE
LEU C:519 , ASN C:520 , ARG C:581
BINDING SITE FOR RESIDUE NAG C 860
16
FC1
SOFTWARE
GLU C:73 , ASN C:75 , ASN C:92
BINDING SITE FOR RESIDUE NAG C 870
17
FC2
SOFTWARE
GLU D:67 , ASN D:85 , SER D:86 , SER D:87 , FUL D:802
BINDING SITE FOR RESIDUE NAG D 800
18
FC3
SOFTWARE
NAG D:800
BINDING SITE FOR RESIDUE FUL D 802
19
FC4
SOFTWARE
ARG D:147 , ASN D:150
BINDING SITE FOR RESIDUE NAG D 810
20
FC5
SOFTWARE
ASN D:219 , THR D:221 , GLN D:308 , GLU D:309 , NAG D:821
BINDING SITE FOR RESIDUE NAG D 820
21
FC6
SOFTWARE
GLU D:309 , GLU D:332 , NAG D:820
BINDING SITE FOR RESIDUE NAG D 821
22
FC7
SOFTWARE
ILE D:194 , ASN D:229 , THR D:231 , GLU D:232 , NAG D:831 , ARG H:33
BINDING SITE FOR RESIDUE NAG D 830
23
FC8
SOFTWARE
NAG D:830 , BMA D:832 , ARG H:34 , GLY H:35
BINDING SITE FOR RESIDUE NAG D 831
24
FC9
SOFTWARE
NAG D:831 , MAN D:833 , GLY H:35
BINDING SITE FOR RESIDUE BMA D 832
25
GC1
SOFTWARE
BMA D:832
BINDING SITE FOR RESIDUE MAN D 833
26
GC2
SOFTWARE
ASN C:450 , TRP D:187 , ASN D:281
BINDING SITE FOR RESIDUE NAG D 840
27
GC3
SOFTWARE
ILE D:319 , ASN D:321 , MET D:348 , SER D:349 , THR D:350 , ARG D:596 , NAG D:851
BINDING SITE FOR RESIDUE NAG D 850
28
GC4
SOFTWARE
ARG D:596 , GLU D:677 , ASP D:678 , NAG D:850
BINDING SITE FOR RESIDUE NAG D 851
29
GC5
SOFTWARE
ASN D:520 , ARG D:581
BINDING SITE FOR RESIDUE NAG D 860
30
GC6
SOFTWARE
GLU D:73 , ASN D:75 , ASN D:92
BINDING SITE FOR RESIDUE NAG D 870
31
GC9
SOFTWARE
HIS G:15 , HIS G:17 , HIS G:214 , ASP G:295
BINDING SITE FOR RESIDUE ZN G 501
32
HC1
SOFTWARE
HIS H:15 , HIS H:17 , HIS H:214 , ASP H:295
BINDING SITE FOR RESIDUE ZN H 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 G/H, )
2: VAR_ADA_BOVIN_002 (T246T, chain G/H, )
3: VAR_ADA_BOVIN_003 (R352R, chain G/H, )
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
---
---
G/H
Q
199
Q
2
UniProt
VAR_ADA_BOVIN_002
*
A
246
T
ADA_BOVIN
---
---
G/H
T
246
T
3
UniProt
VAR_ADA_BOVIN_003
*
G
352
R
ADA_BOVIN
---
---
G/H
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 (G:291-297,H:291-297)
2: 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
A_DEAMINASE
PS00485
Adenosine and AMP deaminase signature.
ADA_BOVIN
291-297
2
-
-
G:291-297
H:291-297
2
PRO_ENDOPEP_SER
PS00708
Prolyl endopeptidase family serine active site.
DPP4_HUMAN
605-635
2
-
-
C:605-635
D: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_d2bgna1 (A:39-508)
1b: SCOP_d2bgnb1 (B:39-508)
1c: SCOP_d2bgnc1 (C:39-508)
1d: SCOP_d2bgnd1 (D:39-508)
2a: SCOP_d2bgna2 (A:509-766)
2b: SCOP_d2bgnb2 (B:509-766)
2c: SCOP_d2bgnc2 (C:509-766)
2d: SCOP_d2bgnd2 (D:509-766)
3a: SCOP_d2bgne1 (E:4-355)
3b: SCOP_d2bgnf1 (F:4-355)
3c: SCOP_d2bgng1 (G:4-355)
3d: SCOP_d2bgnh1 (H:4-355)
View:
Select:
Label:
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
d2bgna1
A:39-508
1b
d2bgnb1
B:39-508
1c
d2bgnc1
C:39-508
1d
d2bgnd1
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
d2bgna2
A:509-766
2b
d2bgnb2
B:509-766
2c
d2bgnc2
C:509-766
2d
d2bgnd2
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
d2bgne1
E:4-355
3b
d2bgnf1
F:4-355
3c
d2bgng1
G:4-355
3d
d2bgnh1
H:4-355
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_2bgnA01 (A:39-51,A:506-766)
1b: CATH_2bgnB01 (B:39-51,B:506-766)
1c: CATH_2bgnC01 (C:39-51,C:506-766)
1d: CATH_2bgnD01 (D:39-51,D:506-766)
2a: CATH_2bgnE00 (E:4-355)
2b: CATH_2bgnF00 (F:4-355)
2c: CATH_2bgnG00 (G:4-355)
2d: CATH_2bgnH00 (H:4-355)
3a: CATH_2bgnA02 (A:55-497)
3b: CATH_2bgnB02 (B:55-497)
3c: CATH_2bgnC02 (C:55-497)
3d: CATH_2bgnD02 (D:55-497)
View:
Select:
Label:
Classes
(
)
(
)
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
2bgnA01
A:39-51,A:506-766
1b
2bgnB01
B:39-51,B:506-766
1c
2bgnC01
C:39-51,C:506-766
1d
2bgnD01
D:39-51,D:506-766
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Human (Homo sapiens)
(5)
2a
2bgnE00
E:4-355
2b
2bgnF00
F:4-355
2c
2bgnG00
G:4-355
2d
2bgnH00
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
2bgnA02
A:55-497
3b
2bgnB02
B:55-497
3c
2bgnC02
C:55-497
3d
2bgnD02
D:55-497
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 C
Chain D
Chain G
Chain H
Chain Y
Chain Z
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
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)
[
close Script example commands
]
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (738 KB)
Header - Asym.Unit
Biol.Unit 1 (366 KB)
Header - Biol.Unit 1
Biol.Unit 2 (366 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2BGN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help