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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4CTH
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (246 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
NEPRILYSIN VARIANT G399V,G714K IN COMPLEX WITH PHOSPHORAMIDON
Authors
:
C. I. Webster, M. Burrell, L. Olsson, S. B. Fowler, S. Digby, A. Sanderco A. Snijder, J. Tebbe, U. Haupts, J. Grudzinska, L. Jermutus, C. Anders
Date
:
13 Mar 14 (Deposition) - 13 Aug 14 (Release) - 13 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Transferase, Amyloid Beta, Alzheimer'S Disease, Enzyme Engineering
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. I. Webster, M. Burrell, L. Olsson, S. B. Fowler, S. Digby, A. Sandercock, A. Snijder, J. Tebbe, U. Haupts, J. Grudzinska, L. Jermutus, C. Andersson
Engineering Neprilysin Activity And Specificity To Create A Novel Therapeutic For Alzheimer'S Disease.
Plos One V. 9 04001 2014
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3a: N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDRO... (RDFa)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
8
Ligand/Ion
GLYCEROL
2
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
RDF
1
Ligand/Ion
N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
4
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:583 , HIS A:587 , GLU A:646 , RDF A:1759
BINDING SITE FOR RESIDUE ZN A1750
02
AC2
SOFTWARE
PHE A:544 , TYR A:545 , GLU A:584 , RDF A:1759
BINDING SITE FOR RESIDUE GOL A1751
03
AC3
SOFTWARE
VAL A:622 , GLY A:626 , LEU A:638 , ASN A:639 , GLY A:640 , ILE A:641 , NAG A:754
BINDING SITE FOR RESIDUE GOL A1752
04
AC4
SOFTWARE
PRO A:482 , ASP A:484 , LYS A:491 , TRP A:534 , HOH A:2171 , HOH A:2220
BINDING SITE FOR RESIDUE GOL A1753
05
AC5
SOFTWARE
CYS A:142 , ILE A:148 , SER A:380 , LYS A:387 , ARG A:409 , TYR A:506 , HOH A:2319
BINDING SITE FOR RESIDUE GOL A1754
06
AC6
SOFTWARE
GLU A:77 , CYS A:79 , HIS A:733 , ARG A:735 , SER A:738 , HOH A:2320
BINDING SITE FOR RESIDUE GOL A1755
07
AC7
SOFTWARE
LEU A:254 , GLN A:257 , GLU A:258 , THR A:385
BINDING SITE FOR RESIDUE GOL A1756
08
AC8
SOFTWARE
PRO A:161 , ASP A:162 , TYR A:164 , GLN A:189 , HOH A:2070
BINDING SITE FOR RESIDUE GOL A1757
09
AC9
SOFTWARE
ARG A:447 , LEU A:473 , ILE A:475 , GLU A:477
BINDING SITE FOR RESIDUE GOL A1758
10
BC1
SOFTWARE
PHE A:106 , VAL A:541 , ASN A:542 , ALA A:543 , ILE A:558 , PHE A:563 , HIS A:583 , GLU A:584 , HIS A:587 , GLU A:646 , TRP A:693 , VAL A:710 , HIS A:711 , ARG A:717 , ZN A:1750 , GOL A:1751 , HOH A:2228 , HOH A:2321
BINDING SITE FOR RESIDUE RDF A1759
11
BC2
SOFTWARE
ASN A:144 , ALA A:147 , HOH A:2318
BINDING SITE FOR MONO-SACCHARIDE NAG A 752 BOUND TO ASN A 144
12
BC3
SOFTWARE
THR A:182 , LYS A:185 , ASN A:324 , GLU A:328
BINDING SITE FOR MONO-SACCHARIDE NAG A 753 BOUND TO ASN A 324
13
BC4
SOFTWARE
THR A:126 , TYR A:623 , GLY A:626 , ASN A:627 , GOL A:1752
BINDING SITE FOR MONO-SACCHARIDE NAG A 754 BOUND TO ASN A 627
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_077685 (C142Y, chain A, )
2: VAR_077686 (Y346C, chain A, )
3: VAR_077687 (A347P, chain A, )
4: VAR_077689 (A421D, chain A, )
5: VAR_077690 (Y496H, chain A, )
6: VAR_077691 (C620R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_077685
C
143
Y
NEP_HUMAN
Disease (SCA43)
879255651
A
C
142
Y
2
UniProt
VAR_077686
Y
347
C
NEP_HUMAN
Disease (CMT2T)
138218277
A
Y
346
C
3
UniProt
VAR_077687
A
348
P
NEP_HUMAN
Unclassified (CMT2T)
199567914
A
A
347
P
4
UniProt
VAR_077689
A
422
D
NEP_HUMAN
Disease (CMT2T)
777476150
A
A
421
D
5
UniProt
VAR_077690
Y
497
H
NEP_HUMAN
Polymorphism
200308207
A
Y
496
H
6
UniProt
VAR_077691
C
621
R
NEP_HUMAN
Disease (CMT2T)
879253752
A
C
620
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:580-589)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
NEP_HUMAN
581-590
1
A:580-589
[
close PROSITE info
]
Exons
(22, 22)
Info
All Exons
Exon 1.9b (A:53-53)
Exon 1.10a (A:53-65)
Exon 1.13c (A:65-119)
Exon 1.14 (A:119-146)
Exon 1.15b (A:146-178)
Exon 1.16 (A:178-217)
Exon 1.17b (A:218-239)
Exon 1.18 (A:240-284)
Exon 1.19 (A:285-318)
Exon 1.20 (A:319-364)
Exon 1.21 (A:364-395)
Exon 1.22 (A:396-438)
Exon 1.23 (A:439-471)
Exon 1.24 (A:472-498)
Exon 1.25 (A:499-533)
Exon 1.26 (A:533-553)
Exon 1.27 (A:553-593)
Exon 1.28 (A:593-637)
Exon 1.29a (A:638-659)
Exon 1.30b (A:660-691)
Exon 1.31 (A:692-717)
Exon 1.32a (A:717-749)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.4d/1.9b
02: Boundary 1.9b/1.10a
03: Boundary 1.10a/1.13c
04: Boundary 1.13c/1.14
05: Boundary 1.14/1.15b
06: Boundary 1.15b/1.16
07: Boundary 1.16/1.17b
08: Boundary 1.17b/1.18
09: Boundary 1.18/1.19
10: Boundary 1.19/1.20
11: Boundary 1.20/1.21
12: Boundary 1.21/1.22
13: Boundary 1.22/1.23
14: Boundary 1.23/1.24
15: Boundary 1.24/1.25
16: Boundary 1.25/1.26
17: Boundary 1.26/1.27
18: Boundary 1.27/1.28
19: Boundary 1.28/1.29a
20: Boundary 1.29a/1.30b
21: Boundary 1.30b/1.31
22: Boundary 1.31/1.32a
23: Boundary 1.32a/-
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
1.4d
ENST00000360490
4d
ENSE00001513376
chr3:
154798188-154798255
68
NEP_HUMAN
-
0
0
-
-
1.9b
ENST00000360490
9b
ENSE00002152527
chr3:
154801947-154802116
170
NEP_HUMAN
1-54
54
1
A:53-53
1
1.10a
ENST00000360490
10a
ENSE00001019489
chr3:
154802848-154802883
36
NEP_HUMAN
54-66
13
1
A:53-65
13
1.13c
ENST00000360490
13c
ENSE00002199839
chr3:
154832783-154832944
162
NEP_HUMAN
66-120
55
1
A:65-119
55
1.14
ENST00000360490
14
ENSE00000934032
chr3:
154834268-154834348
81
NEP_HUMAN
120-147
28
1
A:119-146
28
1.15b
ENST00000360490
15b
ENSE00000934033
chr3:
154834453-154834548
96
NEP_HUMAN
147-179
33
1
A:146-178
33
1.16
ENST00000360490
16
ENSE00000934034
chr3:
154834657-154834775
119
NEP_HUMAN
179-218
40
1
A:178-217
40
1.17b
ENST00000360490
17b
ENSE00000934035
chr3:
154836535-154836600
66
NEP_HUMAN
219-240
22
1
A:218-239
22
1.18
ENST00000360490
18
ENSE00001019488
chr3:
154855891-154856025
135
NEP_HUMAN
241-285
45
1
A:240-284
45
1.19
ENST00000360490
19
ENSE00000934036
chr3:
154857980-154858081
102
NEP_HUMAN
286-319
34
1
A:285-318
34
1.20
ENST00000360490
20
ENSE00000934037
chr3:
154859780-154859916
137
NEP_HUMAN
320-365
46
1
A:319-364
46
1.21
ENST00000360490
21
ENSE00000934038
chr3:
154860026-154860119
94
NEP_HUMAN
365-396
32
1
A:364-395
32
1.22
ENST00000360490
22
ENSE00000934039
chr3:
154861232-154861360
129
NEP_HUMAN
397-439
43
1
A:396-438
43
1.23
ENST00000360490
23
ENSE00000934040
chr3:
154862148-154862246
99
NEP_HUMAN
440-472
33
1
A:439-471
33
1.24
ENST00000360490
24
ENSE00000934041
chr3:
154864933-154865013
81
NEP_HUMAN
473-499
27
1
A:472-498
27
1.25
ENST00000360490
25
ENSE00000779819
chr3:
154866339-154866442
104
NEP_HUMAN
500-534
35
1
A:499-533
35
1.26
ENST00000360490
26
ENSE00000779818
chr3:
154878179-154878237
59
NEP_HUMAN
534-554
21
1
A:533-553
21
1.27
ENST00000360490
27
ENSE00000779817
chr3:
154884691-154884810
120
NEP_HUMAN
554-594
41
1
A:553-593
41
1.28
ENST00000360490
28
ENSE00000779816
chr3:
154886281-154886414
134
NEP_HUMAN
594-638
45
1
A:593-637
45
1.29a
ENST00000360490
29a
ENSE00000779815
chr3:
154886521-154886586
66
NEP_HUMAN
639-660
22
1
A:638-659
22
1.30b
ENST00000360490
30b
ENSE00000779814
chr3:
154889906-154890001
96
NEP_HUMAN
661-692
32
1
A:660-691
32
1.31
ENST00000360490
31
ENSE00000779812
chr3:
154890325-154890401
77
NEP_HUMAN
693-718
26
1
A:692-717
26
1.32a
ENST00000360490
32a
ENSE00001182656
chr3:
154898149-154898277
129
NEP_HUMAN
718-750
33
1
A:717-749
33
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (130 KB)
Header - Asym.Unit
Biol.Unit 1 (246 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
4CTH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
