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.
4H84
Biol. Unit 1
Info
Asym.Unit (75 KB)
Biol.Unit 1 (36 KB)
Biol.Unit 2 (36 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MMP12 IN COMPLEX WITH A SELECTIVE CARBOXYLATE BASED INHIBITOR.
Authors
:
E. A. Stura, C. Antoni, L. Vera, E. Cassar-Lajeunesse, E. Nuti, V. Dive, A. Rossello
Date
:
21 Sep 12 (Deposition) - 24 Apr 13 (Release) - 12 Aug 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.59
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Selective Carboxylate Based Mmp-12 Inhibitor, Metzincin, Zinc Protease, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Antoni, L. Vera, L. Devel, M. P. Catalani, B. Czarny, E. Cassar-Lajeunesse, E. Nuti, A. Rossello, V. Dive, E. A. Stura
Crystallization Of Bi-Functional Ligand Protein Complexes.
J. Struct. Biol. V. 182 246 2013
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
3b: DI(HYDROXYETHYL)ETHER (PEGb)
3c: DI(HYDROXYETHYL)ETHER (PEGc)
4a: S-1,2-PROPANEDIOL (PGOa)
4b: S-1,2-PROPANEDIOL (PGOb)
4c: S-1,2-PROPANEDIOL (PGOc)
4d: S-1,2-PROPANEDIOL (PGOd)
4e: S-1,2-PROPANEDIOL (PGOe)
4f: S-1,2-PROPANEDIOL (PGOf)
4g: S-1,2-PROPANEDIOL (PGOg)
5a: R-1,2-PROPANEDIOL (PGRa)
6a: N-[2-(BENZOYLAMINO)ETHYL]-N-(BIPHE... (Y38a)
6b: N-[2-(BENZOYLAMINO)ETHYL]-N-(BIPHE... (Y38b)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
7c: ZINC ION (ZNc)
7d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
4
PGO
4
Ligand/Ion
S-1,2-PROPANEDIOL
5
PGR
1
Ligand/Ion
R-1,2-PROPANEDIOL
6
Y38
1
Ligand/Ion
N-[2-(BENZOYLAMINO)ETHYL]-N-(BIPHENYL-4-YLSULFONYL)-D-VALINE
7
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(22, 22)
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: CC4 (SOFTWARE)
21: CC7 (SOFTWARE)
22: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:218 , HIS A:222 , HIS A:228 , Y38 A:306
BINDING SITE FOR RESIDUE ZN A 301
02
AC2
SOFTWARE
HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196
BINDING SITE FOR RESIDUE ZN A 302
03
AC3
SOFTWARE
ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:401 , HOH A:406
BINDING SITE FOR RESIDUE CA A 303
04
AC4
SOFTWARE
ASP A:124 , GLU A:199 , GLU A:201 , HOH A:402 , HOH A:471
BINDING SITE FOR RESIDUE CA A 304
05
AC5
SOFTWARE
ASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201
BINDING SITE FOR RESIDUE CA A 305
06
AC6
SOFTWARE
ILE A:180 , LEU A:181 , ALA A:182 , LEU A:214 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , ZN A:301 , PGO A:314 , HIS B:172 , HIS B:183 , ALA B:184 , PHE B:185 , HOH B:423 , HOH B:477
BINDING SITE FOR RESIDUE Y38 A 306
07
AC7
SOFTWARE
ASP A:171 , HIS A:172 , THR B:239 , TYR B:240 , Y38 B:301 , HOH B:485
BINDING SITE FOR RESIDUE PGO A 307
08
AC8
SOFTWARE
LEU A:181 , GLY A:209 , THR A:210 , TYR A:240 , HOH A:501
BINDING SITE FOR RESIDUE PGR A 308
09
AC9
SOFTWARE
GLY A:106 , PRO A:107 , ARG A:110
BINDING SITE FOR RESIDUE PGO A 309
10
BC1
SOFTWARE
PHE A:163 , ALA A:164 , ARG A:165 , SER A:189 , HOH A:419 , HOH A:427 , HOH A:430
BINDING SITE FOR RESIDUE GOL A 310
11
BC2
SOFTWARE
LYS A:111 , MET A:156 , ASP A:158 , ALA A:167 , ASP A:170 , ASP A:171 , HIS A:172 , ALA A:173 , HOH A:405 , HOH A:444 , HOH A:479
BINDING SITE FOR RESIDUE PGO A 311
12
BC3
SOFTWARE
GLY A:225 , GLY A:227 , HIS A:228 , HOH A:418 , HOH A:451 , HOH A:474 , GLY B:225 , GLY B:227
BINDING SITE FOR RESIDUE PEG A 312
13
BC4
SOFTWARE
ARG A:110 , HIS A:112 , ASP A:200 , HOH A:471 , HOH A:517
BINDING SITE FOR RESIDUE PEG A 313
14
BC5
SOFTWARE
GLY A:179 , THR A:239 , TYR A:240 , Y38 A:306 , HOH A:467 , HOH A:475 , ASP B:171 , HIS B:172
BINDING SITE FOR RESIDUE PGO A 314
15
BC6
SOFTWARE
PRO A:123 , HOH A:535
BINDING SITE FOR RESIDUE GOL A 315
16
BC7
SOFTWARE
ARG A:127 , HOH A:505 , ARG B:135
BINDING SITE FOR RESIDUE GOL A 316
17
BC8
SOFTWARE
TRP A:109 , ARG A:110 , HIS A:168 , GLY A:169 , GLY A:188 , HOH A:425 , HOH A:438
BINDING SITE FOR RESIDUE GOL A 317
18
BC9
SOFTWARE
TYR A:132 , THR A:205 , PHE A:213 , ILE A:245 , HOH A:404 , HOH A:468 , HOH A:472 , HOH A:500
BINDING SITE FOR RESIDUE PEG A 318
19
CC1
SOFTWARE
HIS A:172 , HIS A:183 , ALA A:184 , PHE A:185 , PGO A:307 , HOH A:411 , ILE B:180 , LEU B:181 , ALA B:182 , LEU B:214 , HIS B:218 , GLU B:219 , HIS B:222 , HIS B:228 , VAL B:235 , PHE B:237 , PRO B:238 , TYR B:240 , ZN B:302 , GOL B:309 , HOH B:423
BINDING SITE FOR RESIDUE Y38 B 301
20
CC4
SOFTWARE
ARG A:256 , ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:403
BINDING SITE FOR RESIDUE CA B 304
21
CC7
SOFTWARE
ASP A:175 , ASP B:175 , LYS B:177
BINDING SITE FOR RESIDUE PGO B 307
22
DC2
SOFTWARE
LYS A:233 , PRO B:146 , TYR B:262
BINDING SITE FOR RESIDUE GOL B 311
[
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
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d4h84a_ (A:)
1b: SCOP_d4h84b_ (B:)
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
d4h84a_
A:
1b
d4h84b_
B:
[
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 (75 KB)
Header - Asym.Unit
Biol.Unit 1 (36 KB)
Header - Biol.Unit 1
Biol.Unit 2 (36 KB)
Header - Biol.Unit 2
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
4H84
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help