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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3LJZ
Asym. Unit
Info
Asym.Unit (238 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (61 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 HUMAN MMP-13 COMPLEXED WITH AN AMINO-2-INDANOL COMPOUND
Authors
:
H. -S. Shieh, J. R. Kiefer
Date
:
26 Jan 10 (Deposition) - 02 Feb 11 (Release) - 06 Apr 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
:
Mmp-13 Inhibitor; Zinc Chelating Agent; S1' Pocket, Collagen Degradation, Disease Mutation, Disulfide Bond, Extracellular Matrix, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted, Zymogen, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. S. Shieh, A. G. Tomasselli, K. J. Mathis, M. E. Schnute, S. S. Woodard N. Caspers, J. M. Williams, J. R. Kiefer, G. Munie, A. Wittwer, A. M. Malfait, M. D. Tortorella
Structure Analysis Reveals The Flexibility Of The Adamts-5 Active Site.
Protein Sci. V. 20 735 2011
[
close entry info
]
Hetero Components
(5, 33)
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)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
2d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
3a: (2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BE... (LA3a)
3b: (2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BE... (LA3b)
3c: (2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BE... (LA3c)
3d: (2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BE... (LA3d)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
LA3
4
Ligand/Ion
(2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BENZYL]-N~4~-HYDROXY-N~1~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]BUTANEDIAMIDE
4
SO4
9
Ligand/Ion
SULFATE ION
5
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(33, 33)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:161 , ASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:280 , HOH A:340
BINDING SITE FOR RESIDUE CA A 996
02
AC2
SOFTWARE
ASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205
BINDING SITE FOR RESIDUE CA A 997
03
AC3
SOFTWARE
HIS A:172 , ASP A:174 , HIS A:187 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 998
04
AC4
SOFTWARE
HIS A:222 , HIS A:226 , HIS A:232 , LA3 A:801
BINDING SITE FOR RESIDUE ZN A 999
05
AC5
SOFTWARE
HOH A:43 , TYR A:120 , LYS A:139 , ARG A:155
BINDING SITE FOR RESIDUE SO4 A 1
06
AC6
SOFTWARE
LYS A:115 , MET A:116 , ASN A:117
BINDING SITE FOR RESIDUE SO4 A 5
07
AC7
SOFTWARE
LEU A:184 , LEU A:185 , ALA A:186 , LEU A:218 , HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , HOH A:291 , HOH A:292 , ZN A:999
BINDING SITE FOR RESIDUE LA3 A 801
08
AC8
SOFTWARE
ALA B:161 , ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198
BINDING SITE FOR RESIDUE CA B 996
09
AC9
SOFTWARE
ASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205
BINDING SITE FOR RESIDUE CA B 997
10
BC1
SOFTWARE
HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200
BINDING SITE FOR RESIDUE ZN B 998
11
BC2
SOFTWARE
HIS B:222 , HIS B:226 , HIS B:232 , LA3 B:802
BINDING SITE FOR RESIDUE ZN B 999
12
BC3
SOFTWARE
HOH B:4 , HOH B:87 , TYR B:176 , PRO B:190 , ASP B:231 , HIS B:232 , HOH B:277
BINDING SITE FOR RESIDUE EPE B 3
13
BC4
SOFTWARE
HOH B:77 , HOH B:92 , LYS B:139 , ARG B:155 , HOH B:298
BINDING SITE FOR RESIDUE SO4 B 2
14
BC5
SOFTWARE
PRO A:236 , LYS B:115 , MET B:116 , ASN B:117 , HOH B:307 , HOH B:312
BINDING SITE FOR RESIDUE SO4 B 6
15
BC6
SOFTWARE
HOH A:98 , HOH B:4 , GLY B:183 , LEU B:184 , LEU B:185 , ALA B:186 , LEU B:218 , HIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , ALA B:238 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , ZN B:999
BINDING SITE FOR RESIDUE LA3 B 802
16
BC7
SOFTWARE
ALA C:161 , ASP C:162 , ASN C:194 , GLY C:196 , ASP C:198
BINDING SITE FOR RESIDUE CA C 996
17
BC8
SOFTWARE
ASP C:179 , GLY C:180 , SER C:182 , LEU C:184 , ASP C:202 , GLU C:205
BINDING SITE FOR RESIDUE CA C 997
18
BC9
SOFTWARE
HIS C:172 , ASP C:174 , HIS C:187 , HIS C:200
BINDING SITE FOR RESIDUE ZN C 998
19
CC1
SOFTWARE
HIS C:222 , HIS C:226 , HIS C:232 , LA3 C:803
BINDING SITE FOR RESIDUE ZN C 999
20
CC2
SOFTWARE
TYR C:176 , LEU C:184 , HIS C:187 , ALA C:188 , PHE C:189 , PRO C:190
BINDING SITE FOR RESIDUE EPE C 1
21
CC3
SOFTWARE
HOH C:45 , TYR C:120 , LYS C:139 , ARG C:155 , HOH C:311
BINDING SITE FOR RESIDUE SO4 C 3
22
CC4
SOFTWARE
LYS C:115 , MET C:116 , ASN C:117
BINDING SITE FOR RESIDUE SO4 C 7
23
CC5
SOFTWARE
HOH C:10 , LEU C:184 , LEU C:185 , ALA C:186 , LEU C:218 , HIS C:222 , GLU C:223 , HIS C:226 , HIS C:232 , ALA C:238 , LEU C:239 , PHE C:241 , PRO C:242 , ILE C:243 , TYR C:244 , THR C:245 , ZN C:999
BINDING SITE FOR RESIDUE LA3 C 803
24
CC6
SOFTWARE
HOH D:57 , ASP D:162 , ASN D:194 , GLY D:196 , ASP D:198
BINDING SITE FOR RESIDUE CA D 996
25
CC7
SOFTWARE
ASP D:179 , GLY D:180 , SER D:182 , LEU D:184 , ASP D:202 , GLU D:205
BINDING SITE FOR RESIDUE CA D 997
26
CC8
SOFTWARE
HIS D:172 , ASP D:174 , HIS D:187 , HIS D:200
BINDING SITE FOR RESIDUE ZN D 998
27
CC9
SOFTWARE
HIS D:222 , HIS D:226 , HIS D:232 , LA3 D:804
BINDING SITE FOR RESIDUE ZN D 999
28
DC1
SOFTWARE
PRO B:193 , ASN B:194 , TYR D:176 , LEU D:184 , HIS D:187 , PHE D:189 , PRO D:190 , HOH D:289
BINDING SITE FOR RESIDUE EPE D 2
29
DC2
SOFTWARE
GLU D:133 , ALA D:137 , LYS D:140 , SER D:209 , PHE D:217 , HOH D:271 , HOH D:350
BINDING SITE FOR RESIDUE EPE D 4
30
DC3
SOFTWARE
HOH D:7 , LYS D:139 , ARG D:155 , HOH D:321
BINDING SITE FOR RESIDUE SO4 D 268
31
DC4
SOFTWARE
LYS D:115 , MET D:116 , ASN D:117
BINDING SITE FOR RESIDUE SO4 D 8
32
DC5
SOFTWARE
PRO D:108 , ARG D:109
BINDING SITE FOR RESIDUE SO4 D 9
33
DC6
SOFTWARE
HOH D:26 , GLY D:183 , LEU D:184 , LEU D:185 , ALA D:186 , LEU D:218 , HIS D:222 , GLU D:223 , HIS D:226 , HIS D:232 , ALA D:238 , LEU D:239 , PHE D:241 , PRO D:242 , ILE D:243 , TYR D:244 , THR D:245 , HOH D:307 , HOH D:312 , ZN D:999
BINDING SITE FOR RESIDUE LA3 D 804
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_073418 (W207G, chain A/B/C/D, )
2: VAR_063434 (H232N, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_073418
W
207
G
MMP13_HUMAN
Disease (MDST)
---
A/B/C/D
W
207
G
2
UniProt
VAR_063434
H
232
N
MMP13_HUMAN
Disease (MANDP1)
---
A/B/C/D
H
232
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:219-228,B:219-228,C:219-228,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.
MMP13_HUMAN
219-228
4
A:219-228
B:219-228
C:219-228
D:219-228
[
close PROSITE info
]
Exons
(5, 20)
Info
All Exons
Exon 1.2 (A:104-121 | B:104-121 | C:104-121 ...)
Exon 1.3 (A:121-171 | B:121-171 | C:121-171 ...)
Exon 1.4 (A:171-213 | B:171-213 | C:171-213 ...)
Exon 1.5 (A:213-267 (gaps) | B:213-267 | C:2...)
Exon 1.6 (A:267-267 | B:267-267 | C:267-267 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
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
ENST00000260302
1a
ENSE00001105391
chr11:
102826463-102826315
149
MMP13_HUMAN
1-40
40
0
-
-
1.2
ENST00000260302
2
ENSE00001105386
chr11:
102826222-102825981
242
MMP13_HUMAN
41-121
81
4
A:104-121
B:104-121
C:104-121
D:104-121
18
18
18
18
1.3
ENST00000260302
3
ENSE00001105401
chr11:
102825335-102825187
149
MMP13_HUMAN
121-171
51
4
A:121-171
B:121-171
C:121-171
D:121-171
51
51
51
51
1.4
ENST00000260302
4
ENSE00001105398
chr11:
102825010-102824885
126
MMP13_HUMAN
171-213
43
4
A:171-213
B:171-213
C:171-213
D:171-213
43
43
43
43
1.5
ENST00000260302
5
ENSE00001139473
chr11:
102822902-102822741
162
MMP13_HUMAN
213-267
55
4
A:213-267 (gaps)
B:213-267
C:213-267
D:213-267
55
55
55
55
1.6
ENST00000260302
6
ENSE00000930343
chr11:
102820956-102820839
118
MMP13_HUMAN
267-306
40
4
A:267-267
B:267-267
C:267-267
D:267-267
1
1
1
1
1.7
ENST00000260302
7
ENSE00000930342
chr11:
102819887-102819754
134
MMP13_HUMAN
306-351
46
0
-
-
1.8
ENST00000260302
8
ENSE00000930341
chr11:
102818779-102818620
160
MMP13_HUMAN
351-404
54
0
-
-
1.9
ENST00000260302
9
ENSE00000930340
chr11:
102816478-102816375
104
MMP13_HUMAN
404-439
36
0
-
-
1.11b
ENST00000260302
11b
ENSE00002188786
chr11:
102815095-102813724
1372
MMP13_HUMAN
439-471
33
0
-
-
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3ljza_ (A:)
1b: SCOP_d3ljzb_ (B:)
1c: SCOP_d3ljzc_ (C:)
1d: SCOP_d3ljzd_ (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
:
Collagenase-3 (MMP-13)
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
1a
d3ljza_
A:
1b
d3ljzb_
B:
1c
d3ljzc_
C:
1d
d3ljzd_
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_3ljzD01 (D:112-267)
1b: PFAM_Peptidase_M10_3ljzD02 (D:112-267)
1c: PFAM_Peptidase_M10_3ljzD03 (D:112-267)
1d: PFAM_Peptidase_M10_3ljzD04 (D:112-267)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-3ljzD01
D:112-267
1b
Peptidase_M10-3ljzD02
D:112-267
1c
Peptidase_M10-3ljzD03
D:112-267
1d
Peptidase_M10-3ljzD04
D:112-267
[
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 (238 KB)
Header - Asym.Unit
Biol.Unit 1 (60 KB)
Header - Biol.Unit 1
Biol.Unit 2 (61 KB)
Header - Biol.Unit 2
Biol.Unit 3 (60 KB)
Header - Biol.Unit 3
Biol.Unit 4 (61 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
3LJZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
