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.
2WOA
Asym. Unit
Info
Asym.Unit (125 KB)
Biol.Unit 1 (33 KB)
Biol.Unit 2 (33 KB)
Biol.Unit 3 (32 KB)
Biol.Unit 4 (32 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MMP12 COMPLEX WITH A BETA HYDROXY CARBOXYLIC ACID
Authors
:
I. P. Holmes, S. Gaines, S. P. Watson, O. Lorthioir, A. Walker, S. J. Baddeley, S. Herbert, D. Egan, M. A. Convery, O. M. P. Singh, J. W. Gross, J. M. Strelow, R. H. Smith, A. J. Amour, D. Brown, S. L. Martin
Date
:
22 Jul 09 (Deposition) - 08 Sep 09 (Release) - 22 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.26
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
:
Hydrolase, Polymorphism, Glycoprotein, Metal-Binding, Matrix Metalloprotease Mmp-12 Complex Structure, Disulfide Bond, Metalloprotease, Extracellular Matrix, Zinc, Calcium, Zymogen, Protease, Secreted
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. P. Holmes, S. Gaines, S. P. Watson, O. Lorthioir, A. Walker, S. J. Baddeley, S. Herbert, D. Egan, M. A. Convery, O. M. P. Singh, J. W. Gross, J. M. Strelow, R. H. Smith, A. J. Amour, D. Brown, S. L. Martin
The Identification Of Beta-Hydroxy Carboxylic Acids As Selective Mmp-12 Inhibitors.
Bioorg. Med. Chem. Lett. V. 19 5760 2009
[
close entry info
]
Hetero Components
(6, 30)
Info
All Hetero Components
1a: N^2^-[(2R)-2-{(1S)-1-[FORMYL(HYDRO... (023a)
1b: N^2^-[(2R)-2-{(1S)-1-[FORMYL(HYDRO... (023b)
2a: (3S)-5-(9H-FLUOREN-2-YL)-3-HYDROXY... (576a)
2b: (3S)-5-(9H-FLUOREN-2-YL)-3-HYDROXY... (576b)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
3g: CALCIUM ION (CAg)
3h: CALCIUM ION (CAh)
3i: CALCIUM ION (CAi)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
023
2
Ligand/Ion
N^2^-[(2R)-2-{(1S)-1-[FORMYL(HYDROXY)AMINO]ETHYL}-5-PHENYLPENTANOYL]-N,3-DIMETHYL-L-VALINAMIDE
2
576
2
Ligand/Ion
(3S)-5-(9H-FLUOREN-2-YL)-3-HYDROXYPENTANOICACID
3
CA
9
Ligand/Ion
CALCIUM ION
4
GOL
2
Ligand/Ion
GLYCEROL
5
SO4
7
Ligand/Ion
SULFATE ION
6
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(30, 30)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:117 , THR A:154 , GLY A:155
BINDING SITE FOR RESIDUE SO4 A1268
02
AC2
SOFTWARE
ARG B:135 , LYS B:136 , GLN B:139
BINDING SITE FOR RESIDUE SO4 B1268
03
AC3
SOFTWARE
ARG A:135 , LYS A:136 , GLN A:139
BINDING SITE FOR RESIDUE SO4 A1269
04
AC4
SOFTWARE
GLN A:259 , SER A:260 , GLY B:179 , ILE B:180 , LEU B:181 , ALA B:182 , LEU B:214 , THR B:215 , HIS B:218 , GLU B:219 , HIS B:222 , HIS B:228 , PRO B:238 , THR B:239 , TYR B:240 , LYS B:241 , ZN B:1270 , SER D:207 , GOL D:1272
BINDING SITE FOR RESIDUE 023 B1269
05
AC5
SOFTWARE
SER B:207 , GLN C:259 , SER C:260 , GLY D:179 , ILE D:180 , LEU D:181 , ALA D:182 , LEU D:214 , THR D:215 , HIS D:218 , GLU D:219 , HIS D:222 , HIS D:228 , PRO D:238 , THR D:239 , TYR D:240 , LYS D:241 , ZN D:1267 , GOL D:1271 , HOH D:2085 , HOH D:2102 , HOH D:2103
BINDING SITE FOR RESIDUE 023 D1266
06
AC6
SOFTWARE
HIS A:218 , HIS A:222 , HIS A:228 , 576 A:1273
BINDING SITE FOR RESIDUE ZN A1270
07
AC7
SOFTWARE
HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196
BINDING SITE FOR RESIDUE ZN A1271
08
AC8
SOFTWARE
ASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201
BINDING SITE FOR RESIDUE CA A1272
09
AC9
SOFTWARE
HIS B:218 , HIS B:222 , HIS B:228 , 023 B:1269
BINDING SITE FOR RESIDUE ZN B1270
10
BC1
SOFTWARE
HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196
BINDING SITE FOR RESIDUE ZN B1271
11
BC2
SOFTWARE
ASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201
BINDING SITE FOR RESIDUE CA B1272
12
BC3
SOFTWARE
ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:2047 , HOH B:2073
BINDING SITE FOR RESIDUE CA B1273
13
BC4
SOFTWARE
ASP B:124 , GLU B:199 , GLU B:201 , HOH B:2088
BINDING SITE FOR RESIDUE CA B1274
14
BC5
SOFTWARE
HIS C:218 , HIS C:222 , HIS C:228 , 576 C:1273
BINDING SITE FOR RESIDUE ZN C1268
15
BC6
SOFTWARE
HIS C:168 , ASP C:170 , HIS C:183 , HIS C:196
BINDING SITE FOR RESIDUE ZN C1269
16
BC7
SOFTWARE
ASP C:175 , GLY C:176 , GLY C:178 , ILE C:180 , ASP C:198 , GLU C:201
BINDING SITE FOR RESIDUE CA C1270
17
BC8
SOFTWARE
ASP C:158 , GLY C:190 , ILE C:191 , GLY C:192 , ASP C:194
BINDING SITE FOR RESIDUE CA C1271
18
BC9
SOFTWARE
ASP C:124 , GLU C:199 , GLU C:201 , HOH C:2011 , HOH C:2037
BINDING SITE FOR RESIDUE CA C1272
19
CC1
SOFTWARE
HIS D:218 , HIS D:222 , HIS D:228 , 023 D:1266
BINDING SITE FOR RESIDUE ZN D1267
20
CC2
SOFTWARE
HIS D:168 , ASP D:170 , HIS D:183 , HIS D:196
BINDING SITE FOR RESIDUE ZN D1268
21
CC3
SOFTWARE
ASP D:175 , GLY D:176 , GLY D:178 , ILE D:180 , ASP D:198 , GLU D:201
BINDING SITE FOR RESIDUE CA D1269
22
CC4
SOFTWARE
ASP D:124 , GLU D:199 , GLU D:201 , HOH D:2007 , HOH D:2067
BINDING SITE FOR RESIDUE CA D1270
23
CC5
SOFTWARE
LEU A:181 , ALA A:182 , LEU A:214 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , ALA A:234 , VAL A:235 , PHE A:237 , THR A:239 , TYR A:240 , LYS A:241 , ZN A:1270 , HOH A:2103
BINDING SITE FOR RESIDUE 576 A1273
24
CC6
SOFTWARE
LEU C:181 , ALA C:182 , LEU C:214 , HIS C:218 , GLU C:219 , HIS C:222 , HIS C:228 , VAL C:235 , PHE C:237 , PRO C:238 , THR C:239 , TYR C:240 , LYS C:241 , ZN C:1268
BINDING SITE FOR RESIDUE 576 C1273
25
CC7
SOFTWARE
SER B:207 , GLY B:209 , TYR B:240 , TYR B:242 , LEU D:181 , THR D:210 , TYR D:240 , 023 D:1266 , HOH D:2104
BINDING SITE FOR RESIDUE GOL D1271
26
CC8
SOFTWARE
LEU B:181 , THR B:210 , 023 B:1269 , SER D:207 , GLY D:208 , GLY D:209 , TYR D:240 , TYR D:242 , HOH D:2104 , HOH D:2105
BINDING SITE FOR RESIDUE GOL D1272
27
CC9
SOFTWARE
ARG A:110 , HOH A:2104 , HOH A:2105 , HOH A:2106 , ALA B:167 , HIS B:168 , GLY B:169 , ASP B:170 , PHE B:171 , HIS B:172 , ALA B:173 , HOH B:2055
BINDING SITE FOR RESIDUE SO4 A1274
28
DC1
SOFTWARE
ARG C:110 , ALA D:167 , HIS D:168 , GLY D:169 , ASP D:170 , PHE D:171 , HIS D:172 , HOH D:2047 , HOH D:2106 , HOH D:2107
BINDING SITE FOR RESIDUE SO4 D1273
29
DC2
SOFTWARE
THR C:204 , THR C:205 , HIS C:206 , SER C:207 , GLY C:208 , HOH C:2082
BINDING SITE FOR RESIDUE SO4 C1274
30
DC3
SOFTWARE
ALA A:167 , HIS A:168 , GLY A:169 , ASP A:170 , PHE A:171 , HOH A:2050
BINDING SITE FOR RESIDUE SO4 A1275
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:215-224,B:215-224,C:215-224,D:21...)
;
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
4
A:215-224
B:215-224
C:215-224
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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2woaa_ (A:)
1b: SCOP_d2woab_ (B:)
1c: SCOP_d2woac_ (C:)
1d: SCOP_d2woad_ (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
:
Macrophage elastase (MMP-12)
(34)
Human (Homo sapiens) [TaxId: 9606]
(34)
1a
d2woaa_
A:
1b
d2woab_
B:
1c
d2woac_
C:
1d
d2woad_
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_2woaD01 (D:108-263)
1b: PFAM_Peptidase_M10_2woaD02 (D:108-263)
1c: PFAM_Peptidase_M10_2woaD03 (D:108-263)
1d: PFAM_Peptidase_M10_2woaD04 (D:108-263)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-2woaD01
D:108-263
1b
Peptidase_M10-2woaD02
D:108-263
1c
Peptidase_M10-2woaD03
D:108-263
1d
Peptidase_M10-2woaD04
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 A
Chain B
Chain C
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 (125 KB)
Header - Asym.Unit
Biol.Unit 1 (33 KB)
Header - Biol.Unit 1
Biol.Unit 2 (33 KB)
Header - Biol.Unit 2
Biol.Unit 3 (32 KB)
Header - Biol.Unit 3
Biol.Unit 4 (32 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
2WOA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help