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.
2W0D
Biol. Unit 4
Info
Asym.Unit (131 KB)
Biol.Unit 1 (34 KB)
Biol.Unit 2 (33 KB)
Biol.Unit 3 (33 KB)
Biol.Unit 4 (33 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DOES A FAST NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY- AND X-RAY CRYSTALLOGRAPHY HYBRID APPROACH PROVIDE RELIABLE STRUCTURAL INFORMATION OF LIGAND-PROTEIN COMPLEXES? A CASE STUDY OF METALLOPROTEINASES.
Authors
:
J. Isaksson, S. Nystrom, D. J. Derbyshire, H. Wallberg, T. Agback, H. Ko I. Bertini, I. C. Felli
Date
:
13 Aug 08 (Deposition) - 03 Mar 09 (Release) - 28 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Glycoprotein, Metal-Binding, Metalloprotease, Secreted, Hydrolase, Hydroxamate, Extracellular Matrix, Copd, Mmp-12, Zymogen
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Isaksson, S. Nystrom, D. J. Derbyshire, H. Wallberg, T. Agback, H. Kovacs, I. Bertini, I. C. Felli
Does A Fast Nuclear Magnetic Resonance Spectroscopy- And X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information Of Ligand-Protein Complexes? A Case Study Of Metalloproteinases.
J. Med. Chem. V. 52 1712 2009
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
2k: CALCIUM ION (CAk)
2l: CALCIUM ION (CAl)
3a: N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)... (CGSa)
3b: N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)... (CGSb)
3c: N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)... (CGSc)
3d: N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)... (CGSd)
4a: CHLORIDE ION (CLa)
4b: CHLORIDE ION (CLb)
5a: SODIUM ION (NAa)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
6e: ZINC ION (ZNe)
6f: ZINC ION (ZNf)
6g: ZINC ION (ZNg)
6h: ZINC ION (ZNh)
6i: ZINC ION (ZNi)
6j: ZINC ION (ZNj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CGS
1
Ligand/Ion
N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDEHYDROCHLORIDE
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
NA
-1
Ligand/Ion
SODIUM ION
6
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: BC7 (SOFTWARE)
02: BC8 (SOFTWARE)
03: BC9 (SOFTWARE)
04: CC1 (SOFTWARE)
05: CC2 (SOFTWARE)
06: CC3 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC7 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC2 (SOFTWARE)
12: DC3 (SOFTWARE)
13: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC7
SOFTWARE
HIS D:218 , HIS D:222 , HIS D:228 , CGS D:1273
BINDING SITE FOR RESIDUE ZN D1264
02
BC8
SOFTWARE
HIS D:168 , ASP D:170 , HIS D:183 , HIS D:196
BINDING SITE FOR RESIDUE ZN D1265
03
BC9
SOFTWARE
ASP D:175 , GLY D:176 , GLY D:178 , ILE D:180 , ASP D:198 , GLU D:201
BINDING SITE FOR RESIDUE CA D1266
04
CC1
SOFTWARE
ASP D:124 , GLU D:199 , GLU D:201 , HOH D:2108 , HOH D:2112
BINDING SITE FOR RESIDUE CA D1267
05
CC2
SOFTWARE
ASP D:158 , GLY D:190 , GLY D:192 , ASP D:194 , HOH D:2066 , HOH D:2094
BINDING SITE FOR RESIDUE CA D1268
06
CC3
SOFTWARE
HIS A:172 , ACT A:1270 , ACT A:1271 , HIS D:172
BINDING SITE FOR RESIDUE ZN A1269
07
CC4
SOFTWARE
ASP A:170 , PHE A:171 , HIS A:172 , PHE A:185 , ILE A:191 , ZN A:1269 , ACT A:1271 , HIS D:172 , PHE D:185 , HOH D:2075
BINDING SITE FOR RESIDUE ACT A1270
08
CC7
SOFTWARE
THR D:204 , HIS D:206 , SER D:207 , GLY D:208
BINDING SITE FOR RESIDUE CL D1269
09
CC9
SOFTWARE
ALA D:234 , VAL D:235 , PHE D:237 , THR D:239 , HOH D:2143
BINDING SITE FOR RESIDUE NA D1270
10
DC1
SOFTWARE
HIS A:172 , ZN A:1269 , ACT A:1270 , HOH A:2193 , HOH A:2194 , HIS D:172
BINDING SITE FOR RESIDUE ACT A1271
11
DC2
SOFTWARE
ALA D:167 , GLY D:169 , ASP D:170 , PHE D:171 , HOH D:2073 , HOH D:2167
BINDING SITE FOR RESIDUE ACT D1271
12
DC3
SOFTWARE
ARG B:256 , ARG D:110 , HOH D:2009 , HOH D:2168 , HOH D:2169
BINDING SITE FOR RESIDUE ACT D1272
13
DC9
SOFTWARE
ILE D:180 , LEU D:181 , ALA D:182 , HIS D:218 , HIS D:222 , HIS D:228 , PRO D:238 , TYR D:240 , ZN D:1264 , HOH D:2170 , HOH D:2171
BINDING SITE FOR RESIDUE CGS D1273
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (D:215-224)
;
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.
MMP12_HUMAN
215-224
1
-
-
-
D:215-224
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2w0da_ (A:)
1b: SCOP_d2w0db_ (B:)
1c: SCOP_d2w0dc_ (C:)
1d: SCOP_d2w0dd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
Matrix metalloproteases, catalytic domain
(199)
Protein domain
:
automated matches
(32)
Human (Homo sapiens) [TaxId: 9606]
(32)
1a
d2w0da_
A:
1b
d2w0db_
B:
1c
d2w0dc_
C:
1d
d2w0dd_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_2w0dD01 (D:108-263)
1b: PFAM_Peptidase_M10_2w0dD02 (D:108-263)
1c: PFAM_Peptidase_M10_2w0dD03 (D:108-263)
1d: PFAM_Peptidase_M10_2w0dD04 (D:108-263)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-2w0dD01
D:108-263
1b
Peptidase_M10-2w0dD02
D:108-263
1c
Peptidase_M10-2w0dD03
D:108-263
1d
Peptidase_M10-2w0dD04
D:108-263
[
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 D
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 (131 KB)
Header - Asym.Unit
Biol.Unit 1 (34 KB)
Header - Biol.Unit 1
Biol.Unit 2 (33 KB)
Header - Biol.Unit 2
Biol.Unit 3 (33 KB)
Header - Biol.Unit 3
Biol.Unit 4 (33 KB)
Header - Biol.Unit 4
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
2W0D
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help