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.
PLEASE WAIT...
Getting 'Exon' information from database.
1ITU
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (131 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN RENAL DIPEPTIDASE COMPLEXED WITH CILASTATIN
Authors
:
Y. Nitanai, Y. Satow, H. Adachi, M. Tsujimoto
Date
:
03 Feb 02 (Deposition) - 28 Aug 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Dipeptidase, Glycoprotein, Membrane-Bound, Zinc Protease Beta- Lactamase, Cilastatin, Complex (Hydrolase-Inhibitor), Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Nitanai, Y. Satow, H. Adachi, M. Tsujimoto
Crystal Structure Of Human Renal Dipeptidase Involved In Beta-Lactam Hydrolysis
J. Mol. Biol. V. 321 177 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: CILASTATIN (CILa)
1b: CILASTATIN (CILb)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIL
2
Ligand/Ion
CILASTATIN
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:41 , THR A:43 , MET A:95 , HOH A:1290 , HOH A:1343
BINDING SITE FOR RESIDUE NAG A 461
02
AC2
SOFTWARE
GLU B:38 , ASN B:41 , THR B:43 , HOH B:1515
BINDING SITE FOR RESIDUE NAG B 462
03
AC3
SOFTWARE
ASN A:316 , HOH B:1107
BINDING SITE FOR RESIDUE NAG A 463
04
AC4
SOFTWARE
PHE A:2 , GLU A:6 , ASN B:316 , THR B:318 , HOH B:1489 , HOH B:1601
BINDING SITE FOR RESIDUE NAG B 464
05
AC5
SOFTWARE
HIS A:20 , ASP A:22 , GLU A:125 , ZN A:402 , HOH A:421 , CIL A:451
BINDING SITE FOR RESIDUE ZN A 401
06
AC6
SOFTWARE
GLU A:125 , HIS A:198 , HIS A:219 , ZN A:401 , HOH A:421 , CIL A:451
BINDING SITE FOR RESIDUE ZN A 402
07
AC7
SOFTWARE
HIS B:20 , ASP B:22 , GLU B:125 , ZN B:412 , HOH B:422 , CIL B:452
BINDING SITE FOR RESIDUE ZN B 411
08
AC8
SOFTWARE
GLU B:125 , HIS B:198 , HIS B:219 , ZN B:411 , HOH B:422 , CIL B:452
BINDING SITE FOR RESIDUE ZN B 412
09
AC9
SOFTWARE
ASP A:22 , TYR A:68 , HIS A:152 , HIS A:198 , HIS A:219 , ARG A:230 , TYR A:252 , TYR A:255 , ASP A:288 , GLY A:291 , PRO A:293 , ZN A:401 , ZN A:402 , HOH A:421
BINDING SITE FOR RESIDUE CIL A 451
10
BC1
SOFTWARE
ASP B:22 , TYR B:68 , HIS B:152 , HIS B:198 , HIS B:219 , ARG B:230 , TYR B:255 , ASP B:288 , GLY B:291 , VAL B:292 , ZN B:411 , ZN B:412 , HOH B:422
BINDING SITE FOR RESIDUE CIL B 452
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036496 (R230H, chain A/B, )
2: VAR_DPEP1_HUMAN_CCDS10982_1_01 (R230H, chain A/B, )
3: VAR_061375 (E335K, chain A/B, )
4: VAR_061376 (E335Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_036496
R
246
H
DPEP1_HUMAN
Unclassified
---
A/B
R
230
H
2
CancerSNP
VAR_DPEP1_HUMAN_CCDS10982_1_01
*
R
246
H
DPEP1_HUMAN
Disease (Colorectal cancer)
---
A/B
R
230
H
3
UniProt
VAR_061375
E
351
K
DPEP1_HUMAN
Polymorphism
1126464
A/B
E
335
K
4
UniProt
VAR_061376
E
351
Q
DPEP1_HUMAN
Polymorphism
1126464
A/B
E
335
Q
* 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: RENAL_DIPEPTIDASE_2 (A:1-369,B:1-369)
2: RENAL_DIPEPTIDASE_1 (A:124-146,B:124-146)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RENAL_DIPEPTIDASE_2
PS51365
Renal dipeptidase family profile.
DPEP1_HUMAN
17-385
2
A:1-369
B:1-369
2
RENAL_DIPEPTIDASE_1
PS00869
Renal dipeptidase active site.
DPEP1_HUMAN
140-162
2
A:124-146
B:124-146
[
close PROSITE info
]
Exons
(10, 20)
Info
All Exons
Exon 1.3b (A:1-19 | B:1-19)
Exon 1.4 (A:19-63 | B:19-63)
Exon 1.5 (A:64-108 | B:64-108)
Exon 1.6 (A:108-158 | B:108-158)
Exon 1.7 (A:158-181 | B:158-181)
Exon 1.8 (A:182-240 | B:182-240)
Exon 1.9 (A:241-269 | B:241-269)
Exon 1.10 (A:269-294 | B:269-294)
Exon 1.11 (A:294-339 | B:294-339)
Exon 1.12a (A:340-369 | B:340-369)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2/1.3b
02: Boundary 1.3b/1.4
03: Boundary 1.4/1.5
04: Boundary 1.5/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/1.12a
11: Boundary 1.12a/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.2
ENST00000393092
2
ENSE00001514166
chr16:
89687000-89687184
185
DPEP1_HUMAN
-
0
0
-
-
1.3b
ENST00000393092
3b
ENSE00000946266
chr16:
89696713-89696922
210
DPEP1_HUMAN
1-35
35
2
A:1-19
B:1-19
19
19
1.4
ENST00000393092
4
ENSE00001312895
chr16:
89702316-89702448
133
DPEP1_HUMAN
35-79
45
2
A:19-63
B:19-63
45
45
1.5
ENST00000393092
5
ENSE00001290840
chr16:
89702672-89702804
133
DPEP1_HUMAN
80-124
45
2
A:64-108
B:64-108
45
45
1.6
ENST00000393092
6
ENSE00001314206
chr16:
89702941-89703091
151
DPEP1_HUMAN
124-174
51
2
A:108-158
B:108-158
51
51
1.7
ENST00000393092
7
ENSE00001292209
chr16:
89703274-89703343
70
DPEP1_HUMAN
174-197
24
2
A:158-181
B:158-181
24
24
1.8
ENST00000393092
8
ENSE00001325387
chr16:
89703612-89703788
177
DPEP1_HUMAN
198-256
59
2
A:182-240
B:182-240
59
59
1.9
ENST00000393092
9
ENSE00001292673
chr16:
89703876-89703960
85
DPEP1_HUMAN
257-285
29
2
A:241-269
B:241-269
29
29
1.10
ENST00000393092
10
ENSE00001305962
chr16:
89704040-89704115
76
DPEP1_HUMAN
285-310
26
2
A:269-294
B:269-294
26
26
1.11
ENST00000393092
11
ENSE00001314382
chr16:
89704244-89704379
136
DPEP1_HUMAN
310-355
46
2
A:294-339
B:294-339
46
46
1.12a
ENST00000393092
12a
ENSE00001307235
chr16:
89704460-89704838
379
DPEP1_HUMAN
356-411
56
2
A:340-369
B:340-369
30
30
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1itua_ (A:)
1b: SCOP_d1itub_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Renal dipeptidase
(2)
Protein domain
:
Renal dipeptidase
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1itua_
A:
1b
d1itub_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1ituA00 (A:1-369)
1b: CATH_1ituB00 (B:1-369)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Human (Homo sapiens)
(5)
1a
1ituA00
A:1-369
1b
1ituB00
B:1-369
[
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 A
Chain B
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 (136 KB)
Header - Asym.Unit
Biol.Unit 1 (131 KB)
Header - Biol.Unit 1
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
1ITU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
