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.
1B8Y
Asym. Unit
Info
Asym.Unit (36 KB)
Biol.Unit 1 (31 KB)
Biol.Unit 2 (60 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 STROMELYSIN CATALYTIC DOMAIN COMPLEXED WITH NON-PEPTIDE INHIBITORS: IMPLICATIONS FOR INHIBITOR SELECTIVITY
Authors
:
A. G. Pavlovsky, M. G. Williams, Q. -Z. Ye, D. F. Ortwine, C. F. Purchase A. D. White, V. Dhanaraj, B. D. Roth, L. L. Johnson, D. Hupe, C. Humblet, T. L. Blundell
Date
:
03 Feb 99 (Deposition) - 31 Aug 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Hydrolase, Matrix Metalloproteinase-3, Stromelysin-1
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Pavlovsky, M. G. Williams, Q. Z. Ye, D. F. Ortwine, C. F. Purchase 2Nd. , A. D. White, V. Dhanaraj, B. D. Roth, L. L. Johnson D. Hupe, C. Humblet, T. L. Blundell
X-Ray Structure Of Human Stromelysin Catalytic Domain Complexed With Nonpeptide Inhibitors: Implications For Inhibitor Selectivity.
Protein Sci. V. 8 1455 1999
[
close entry info
]
Hetero Components
(4, 7)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: [4-(4-PHENYL-PIPERIDIN-1-YL)-BENZE... (IN7a)
3a: SULFATE ION (SO4a)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
3
Ligand/Ion
CALCIUM ION
2
IN7
1
Ligand/Ion
[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-ACETIC ACID
3
SO4
1
Ligand/Ion
SULFATE ION
4
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
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: CA1 (AUTHOR)
09: CA2 (AUTHOR)
10: CA3 (AUTHOR)
11: IN7 (AUTHOR)
12: ZN1 (AUTHOR)
13: ZN2 (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:201 , HIS A:205 , HIS A:211 , IN7 A:502
BINDING SITE FOR RESIDUE ZN A 301
02
AC2
SOFTWARE
HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179
BINDING SITE FOR RESIDUE ZN A 302
03
AC3
SOFTWARE
ASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184
BINDING SITE FOR RESIDUE CA A 303
04
AC4
SOFTWARE
ASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:403 , HOH A:404
BINDING SITE FOR RESIDUE CA A 304
05
AC5
SOFTWARE
ASP A:107 , ASP A:182 , GLU A:184 , HOH A:401
BINDING SITE FOR RESIDUE CA A 305
06
AC6
SOFTWARE
PRO A:109 , LYS A:110 , HOH A:444
BINDING SITE FOR RESIDUE SO4 A 501
07
AC7
SOFTWARE
LEU A:164 , ALA A:165 , HIS A:201 , GLU A:202 , HIS A:211 , ALA A:217 , LEU A:218 , TYR A:220 , PRO A:221 , LEU A:222 , TYR A:223 , HIS A:224 , ZN A:301 , HOH A:406
BINDING SITE FOR RESIDUE IN7 A 502
08
CA1
AUTHOR
ASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184
CA1 IS THE FIRST CALCIUM BINDING SITE OF CA 303.
09
CA2
AUTHOR
ASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:403 , HOH A:404
CA2 IS THE SECOND CALCIUM BINDING SITE OF CA 304.
10
CA3
AUTHOR
ASP A:107 , ASP A:182 , GLU A:184 , HOH A:401
CA3 IS THE THIRD CALCIUM BINDING SITE OF CA 305.
11
IN7
AUTHOR
IN7 A:502
IN7 IS THE BINDING SITE FOR THE DIPHENYLPIPERIDINE SULFONAMIDE INHIBITOR.
12
ZN1
AUTHOR
HIS A:201 , HIS A:205 , HIS A:211 , IN7 A:502
ZN1 IS THE CATALYTIC ZINC BINDING SITE OF ZN 301.
13
ZN2
AUTHOR
HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179
ZN2 IS THE STRUCTURAL ZINC BINDING SITE OF ZN 302.
[
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, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:198-207)
;
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.
MMP3_HUMAN
215-224
1
A:198-207
[
close PROSITE info
]
Exons
(5, 5)
Info
All Exons
Exon 1.2 (A:83-100)
Exon 1.3 (A:100-150)
Exon 1.4b (A:150-192)
Exon 1.5 (A:192-247)
Exon 1.6 (A:247-249)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4b
4: Boundary 1.4b/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
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
1.1a
ENST00000299855
1a
ENSE00002171374
chr11:
102714534-102714173
362
MMP3_HUMAN
1-35
35
0
-
-
1.2
ENST00000299855
2
ENSE00001105428
chr11:
102713647-102713403
245
MMP3_HUMAN
36-117
82
1
A:83-100
18
1.3
ENST00000299855
3
ENSE00001642002
chr11:
102713310-102713162
149
MMP3_HUMAN
117-167
51
1
A:100-150
51
1.4b
ENST00000299855
4b
ENSE00001105420
chr11:
102713010-102712885
126
MMP3_HUMAN
167-209
43
1
A:150-192
43
1.5
ENST00000299855
5
ENSE00001657829
chr11:
102711324-102711160
165
MMP3_HUMAN
209-264
56
1
A:192-247
56
1.6
ENST00000299855
6
ENSE00001105427
chr11:
102710983-102710839
145
MMP3_HUMAN
264-312
49
1
A:247-249
3
1.7
ENST00000299855
7
ENSE00001105439
chr11:
102709974-102709841
134
MMP3_HUMAN
312-357
46
0
-
-
1.8
ENST00000299855
8
ENSE00001801971
chr11:
102709441-102709282
160
MMP3_HUMAN
357-410
54
0
-
-
1.9
ENST00000299855
9
ENSE00001105448
chr11:
102708132-102708029
104
MMP3_HUMAN
410-445
36
0
-
-
1.11
ENST00000299855
11
ENSE00001292630
chr11:
102706957-102706532
426
MMP3_HUMAN
445-477
33
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1b8ya_ (A:)
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
:
Stromelysin-1 (MMP-3)
(40)
Human (Homo sapiens), fibroblast [TaxId: 9606]
(40)
1a
d1b8ya_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1b8yA00 (A:83-249)
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
1b8yA00
A:83-249
[
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 (36 KB)
Header - Asym.Unit
Biol.Unit 1 (31 KB)
Header - Biol.Unit 1
Biol.Unit 2 (60 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
1B8Y
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
