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.
1OS2
Asym. Unit
Info
Asym.Unit (178 KB)
Biol.Unit 1 (32 KB)
Biol.Unit 2 (33 KB)
Biol.Unit 3 (33 KB)
Biol.Unit 4 (32 KB)
Biol.Unit 5 (32 KB)
Biol.Unit 6 (32 KB)
Biol.Unit 7 (86 KB)
Biol.Unit 8 (87 KB)
Biol.Unit 9 (59 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TERNARY ENZYME-PRODUCT-INHIBITOR COMPLEXES OF HUMAN MMP12
Authors
:
I. Bertini, V. Calderone, M. Fragai, C. Luchinat, S. Mangani, B. Terni
Date
:
18 Mar 03 (Deposition) - 05 Aug 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: D,E,F (1x)
Biol. Unit 8: A,B,C (1x)
Biol. Unit 9: A,C (1x)
Keywords
:
Matrix Metalloproteinase, Hydroxamic Acid, Mmp12, Elastase, Complex (Elastase/Inhibitor), Metallo Elastase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Bertini, V. Calderone, M. Fragai, C. Luchinat, S. Mangani, B. Terni
X-Ray Structures Of Binary And Ternary Enzyme-Product-Inhibitor Complexes Of Matrix Metalloproteinases
Angew. Chem. Int. Ed. Engl. V. 42 2673 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 36)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: AZIDE ION (AZIa)
2b: AZIDE ION (AZIb)
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)
3j: CALCIUM ION (CAj)
3k: CALCIUM ION (CAk)
3l: CALCIUM ION (CAl)
3m: CALCIUM ION (CAm)
3n: CALCIUM ION (CAn)
3o: CALCIUM ION (CAo)
3p: CALCIUM ION (CAp)
3q: CALCIUM ION (CAq)
3r: CALCIUM ION (CAr)
4a: ACETOHYDROXAMIC ACID (HAEa)
4b: ACETOHYDROXAMIC ACID (HAEb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
5i: ZINC ION (ZNi)
5j: ZINC ION (ZNj)
5k: ZINC ION (ZNk)
5l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
AZI
2
Ligand/Ion
AZIDE ION
3
CA
18
Ligand/Ion
CALCIUM ION
4
HAE
2
Ligand/Ion
ACETOHYDROXAMIC ACID
5
ZN
12
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(36, 36)
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)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:218 , HIS A:222 , HIS A:228 , HAE A:874
BINDING SITE FOR RESIDUE ZN A 869
02
AC2
SOFTWARE
HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196
BINDING SITE FOR RESIDUE ZN A 870
03
AC3
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 871
04
AC4
SOFTWARE
ASP A:158 , GLY A:190 , GLY A:192 , ASP A:194
BINDING SITE FOR RESIDUE CA A 872
05
AC5
SOFTWARE
ASP A:124 , GLU A:199 , GLU A:201
BINDING SITE FOR RESIDUE CA A 873
06
AC6
SOFTWARE
HIS B:218 , HIS B:222 , HIS B:228 , ACT B:374
BINDING SITE FOR RESIDUE ZN B 369
07
AC7
SOFTWARE
HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196
BINDING SITE FOR RESIDUE ZN B 370
08
AC8
SOFTWARE
ASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201
BINDING SITE FOR RESIDUE CA B 371
09
AC9
SOFTWARE
ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:397
BINDING SITE FOR RESIDUE CA B 372
10
BC1
SOFTWARE
ASP B:124 , GLU B:199 , GLU B:201 , HOH B:393 , HOH B:430
BINDING SITE FOR RESIDUE CA B 373
11
BC2
SOFTWARE
MET A:104 , HIS B:222 , HIS B:228 , ZN B:369 , HOH B:434
BINDING SITE FOR RESIDUE ACT B 374
12
BC3
SOFTWARE
MET B:104 , HIS C:218 , HIS C:222 , HIS C:228 , AZI C:474
BINDING SITE FOR RESIDUE ZN C 469
13
BC4
SOFTWARE
HIS C:168 , ASP C:170 , HIS C:183 , HIS C:196
BINDING SITE FOR RESIDUE ZN C 470
14
BC5
SOFTWARE
ASP C:175 , GLY C:176 , GLY C:178 , ILE C:180 , ASP C:198 , GLU C:201
BINDING SITE FOR RESIDUE CA C 471
15
BC6
SOFTWARE
ASP C:158 , GLY C:190 , GLY C:192 , ASP C:194 , HOH C:494 , HOH C:520
BINDING SITE FOR RESIDUE CA C 472
16
BC7
SOFTWARE
HOH A:905 , ASP C:124 , GLU C:199 , GLU C:201 , HOH C:506
BINDING SITE FOR RESIDUE CA C 473
17
BC8
SOFTWARE
MET B:104 , HIS C:218 , GLU C:219 , HIS C:222 , HIS C:228 , ZN C:469
BINDING SITE FOR RESIDUE AZI C 474
18
BC9
SOFTWARE
HIS D:218 , HIS D:222 , HIS D:228 , HAE D:574
BINDING SITE FOR RESIDUE ZN D 569
19
CC1
SOFTWARE
HIS D:168 , ASP D:170 , HIS D:183 , HIS D:196
BINDING SITE FOR RESIDUE ZN D 570
20
CC2
SOFTWARE
ASP D:175 , GLY D:176 , GLY D:178 , ILE D:180 , ASP D:198 , GLU D:201
BINDING SITE FOR RESIDUE CA D 571
21
CC3
SOFTWARE
ASP D:158 , GLY D:190 , GLY D:192 , ASP D:194 , HOH D:598
BINDING SITE FOR RESIDUE CA D 572
22
CC4
SOFTWARE
ASP D:124 , GLU D:199 , GLU D:201
BINDING SITE FOR RESIDUE CA D 573
23
CC5
SOFTWARE
HIS E:218 , HIS E:222 , HIS E:228 , ACT E:674
BINDING SITE FOR RESIDUE ZN E 669
24
CC6
SOFTWARE
HIS E:168 , ASP E:170 , HIS E:183 , HIS E:196
BINDING SITE FOR RESIDUE ZN E 670
25
CC7
SOFTWARE
ASP E:175 , GLY E:176 , GLY E:178 , ILE E:180 , ASP E:198 , GLU E:201
BINDING SITE FOR RESIDUE CA E 671
26
CC8
SOFTWARE
ASP E:158 , GLY E:190 , GLY E:192 , ASP E:194
BINDING SITE FOR RESIDUE CA E 672
27
CC9
SOFTWARE
ASP E:124 , GLU E:199 , GLU E:201 , HOH E:708
BINDING SITE FOR RESIDUE CA E 673
28
DC1
SOFTWARE
MET D:104 , ALA E:182 , HIS E:218 , GLU E:219 , HIS E:222 , HIS E:228 , ZN E:669 , HOH E:722
BINDING SITE FOR RESIDUE ACT E 674
29
DC2
SOFTWARE
MET E:104 , HIS F:218 , HIS F:222 , HIS F:228 , AZI F:774
BINDING SITE FOR RESIDUE ZN F 769
30
DC3
SOFTWARE
HIS F:168 , ASP F:170 , HIS F:183 , HIS F:196
BINDING SITE FOR RESIDUE ZN F 770
31
DC4
SOFTWARE
ASP F:175 , GLY F:176 , GLY F:178 , ILE F:180 , ASP F:198 , GLU F:201
BINDING SITE FOR RESIDUE CA F 771
32
DC5
SOFTWARE
ASP F:158 , GLY F:190 , GLY F:192 , ASP F:194 , HOH F:786 , HOH F:812
BINDING SITE FOR RESIDUE CA F 772
33
DC6
SOFTWARE
ASP F:124 , GLU F:199 , GLU F:201 , HOH F:802
BINDING SITE FOR RESIDUE CA F 773
34
DC7
SOFTWARE
MET E:104 , HIS F:218 , HIS F:222 , HIS F:228 , ZN F:769
BINDING SITE FOR RESIDUE AZI F 774
35
DC8
SOFTWARE
ALA A:182 , HIS A:183 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , ZN A:869 , HOH A:894 , HOH A:919 , MET C:104
BINDING SITE FOR RESIDUE HAE A 874
36
DC9
SOFTWARE
ALA D:182 , HIS D:183 , HIS D:218 , GLU D:219 , HIS D:222 , HIS D:228 , ZN D:569 , HOH D:586 , HOH D:607 , MET F:104
BINDING SITE FOR RESIDUE HAE D 574
[
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, 6)
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
6
A:215-224
B:215-224
C:215-224
D:215-224
E:215-224
F: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, 6)
Info
All SCOP Domains
1a: SCOP_d1os2a_ (A:)
1b: SCOP_d1os2b_ (B:)
1c: SCOP_d1os2c_ (C:)
1d: SCOP_d1os2d_ (D:)
1e: SCOP_d1os2e_ (E:)
1f: SCOP_d1os2f_ (F:)
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
d1os2a_
A:
1b
d1os2b_
B:
1c
d1os2c_
C:
1d
d1os2d_
D:
1e
d1os2e_
E:
1f
d1os2f_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1os2A00 (A:104-268)
1b: CATH_1os2B00 (B:104-268)
1c: CATH_1os2C00 (C:104-268)
1d: CATH_1os2D00 (D:104-268)
1e: CATH_1os2E00 (E:104-268)
1f: CATH_1os2F00 (F:104-268)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Collagenase (Catalytic Domain)
(236)
Homologous Superfamily
:
Collagenase (Catalytic Domain)
(234)
Human (Homo sapiens)
(153)
1a
1os2A00
A:104-268
1b
1os2B00
B:104-268
1c
1os2C00
C:104-268
1d
1os2D00
D:104-268
1e
1os2E00
E:104-268
1f
1os2F00
F:104-268
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_1os2F01 (F:108-263)
1b: PFAM_Peptidase_M10_1os2F02 (F:108-263)
1c: PFAM_Peptidase_M10_1os2F03 (F:108-263)
1d: PFAM_Peptidase_M10_1os2F04 (F:108-263)
1e: PFAM_Peptidase_M10_1os2F05 (F:108-263)
1f: PFAM_Peptidase_M10_1os2F06 (F:108-263)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-1os2F01
F:108-263
1b
Peptidase_M10-1os2F02
F:108-263
1c
Peptidase_M10-1os2F03
F:108-263
1d
Peptidase_M10-1os2F04
F:108-263
1e
Peptidase_M10-1os2F05
F:108-263
1f
Peptidase_M10-1os2F06
F: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
Chain E
Chain F
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 (178 KB)
Header - Asym.Unit
Biol.Unit 1 (32 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 (32 KB)
Header - Biol.Unit 4
Biol.Unit 5 (32 KB)
Header - Biol.Unit 5
Biol.Unit 6 (32 KB)
Header - Biol.Unit 6
Biol.Unit 7 (86 KB)
Header - Biol.Unit 7
Biol.Unit 8 (87 KB)
Header - Biol.Unit 8
Biol.Unit 9 (59 KB)
Header - Biol.Unit 9
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
1OS2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help