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.
3N7O
Asym. Unit
Info
Asym.Unit (46 KB)
Biol.Unit 1 (41 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH SMALL MOLECULE INHIBITOR.
Authors
:
M. C. Abad, J. Kervinen, C. Crysler, S. Bayoumy, J. Spurlino, I. Deckman M. N. Greco, B. E. Maryanoff, L. Degaravilla
Date
:
27 May 10 (Deposition) - 21 Jul 10 (Release) - 01 Sep 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Serine Protease, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Kervinen, C. Crysler, S. Bayoumy, M. C. Abad, J. Spurlino, I. Deckman, M. N. Greco, B. E. Maryanoff, L. De Garavilla
Potency Variation Of Small-Molecule Chymase Inhibitors Across Species.
Biochem Pharmacol V. 80 1033 2010
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: (S)-[(1S)-1-(5-CHLORO-1-BENZOTHIOP... (N7Oa)
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: UNKNOWN LIGAND (UNLa)
3b: UNKNOWN LIGAND (UNLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
N7O
1
Ligand/Ion
(S)-[(1S)-1-(5-CHLORO-1-BENZOTHIOPHEN-3-YL)-2-{[(E)-2-(3,4-DIFLUOROPHENYL)ETHENYL]AMINO}-2-OXOETHYL]METHYLPHOSPHINIC ACID
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
UNL
2
Ligand/Ion
UNKNOWN LIGAND
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:40 , HIS A:57 , TYR A:94 , ASN A:95 , THR A:96 , LEU A:99 , ASP A:102 , ALA A:190 , PHE A:191 , LYS A:192 , GLY A:193 , SER A:195 , VAL A:213 , SER A:214 , TYR A:215 , GLY A:216 , ARG A:217
BINDING SITE FOR RESIDUE N7O A 1
2
AC2
SOFTWARE
NAG A:2 , ASN A:72 , THR A:74 , GLU A:75 , ASP A:153 , GLN A:243 , HOH A:335
BINDING SITE FOR RESIDUE NAG A 246
3
AC3
SOFTWARE
ASN A:239 , GLN A:243 , NAG A:246 , HOH A:320 , HOH A:376
BINDING SITE FOR RESIDUE NAG A 2
4
AC4
SOFTWARE
ASN A:95 , NAG A:248 , HOH A:295
BINDING SITE FOR RESIDUE NAG A 247
5
AC5
SOFTWARE
NAG A:247
BINDING SITE FOR RESIDUE NAG A 248
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011770 (G37R, chain A, )
2: VAR_011771 (H57R, chain A, )
3: VAR_029190 (R90H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011770
G
46
R
CMA1_HUMAN
Polymorphism
5246
A
G
37
R
2
UniProt
VAR_011771
H
66
R
CMA1_HUMAN
Polymorphism
5247
A
H
57
R
3
UniProt
VAR_029190
R
98
H
CMA1_HUMAN
Polymorphism
13306252
A
R
90
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (A:16-243)
2: TRYPSIN_HIS (A:53-58)
3: TRYPSIN_SER (A:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
CMA1_HUMAN
22-245
1
A:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
CMA1_HUMAN
62-67
1
A:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
CMA1_HUMAN
197-208
1
A:189-200
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.2a (A:16-61)
Exon 1.3 (A:61-107 (gaps))
Exon 1.4a (A:108-192 (gaps))
Exon 1.5b (A:193-245 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4a
4: Boundary 1.4a/1.5b
5: Boundary 1.5b/-
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
1.1
ENST00000250378
1
ENSE00001144725
chr14:
24977471-24977384
88
CMA1_HUMAN
1-20
20
0
-
-
1.2a
ENST00000250378
2a
ENSE00001144738
chr14:
24976712-24976562
151
CMA1_HUMAN
20-70
51
1
A:16-61
49
1.3
ENST00000250378
3
ENSE00000586440
chr14:
24975810-24975675
136
CMA1_HUMAN
70-115
46
1
A:61-107 (gaps)
48
1.4a
ENST00000250378
4a
ENSE00000654524
chr14:
24975488-24975234
255
CMA1_HUMAN
116-200
85
1
A:108-192 (gaps)
88
1.5b
ENST00000250378
5b
ENSE00001816406
chr14:
24974865-24974561
305
CMA1_HUMAN
201-247
47
1
A:193-245 (gaps)
53
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3n7oa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Chymase (mast cell protease I)
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d3n7oa_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Trypsin_3n7oA01 (A:16-238)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Homo sapiens (Human)
(339)
1a
Trypsin-3n7oA01
A:16-238
[
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 (46 KB)
Header - Asym.Unit
Biol.Unit 1 (41 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
3N7O
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
