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.
2JIH
Asym. Unit
Info
Asym.Unit (105 KB)
Biol.Unit 1 (51 KB)
Biol.Unit 2 (50 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 ADAMTS-1 CATALYTIC DOMAIN AND CYSTEINE-RICH DOMAIN (COMPLEX-FORM)
Authors
:
S. Gerhardt, G. Hassall, P. Hawtin, E. Mccall, L. Flavell, C. Minshull, D. Hargreaves, A. Ting, R. A. Pauptit, A. E. Parker, W. M. Abbott
Date
:
28 Jun 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Zinc, Zymogen, Protease, Adamts-1, Hydrolase, Metalloprotease, Heparin-Binding, Metalloproteinase, Metzincin, Polymorphism, Glycoprotein, Metal-Binding, Extracellular Matrix, Cleavage On Pair Of Basic Residues
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Gerhardt, G. Hassall, P. Hawtin, E. Mccall, L. Flavell, C. Minshull, D. Hargreaves, A. Ting, R. A. Pauptit, A. E. Parker, W. M. Abbott
Crystal Structures Of Human Adamts-1 Reveal A Conserved Catalytic Domain And A Disintegrin-Like Domain With A Fold Homologous To Cysteine-Rich Domains.
J. Mol. Biol. V. 373 891 2007
[
close entry info
]
Hetero Components
(6, 33)
Info
All Hetero Components
1a: (2S,3R)-N~4~-[(1S)-2,2-DIMETHYL-1-... (097a)
1b: (2S,3R)-N~4~-[(1S)-2,2-DIMETHYL-1-... (097b)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
2c: CADMIUM ION (CDc)
2d: CADMIUM ION (CDd)
2e: CADMIUM ION (CDe)
2f: CADMIUM ION (CDf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
5a: NICKEL (II) ION (NIa)
5b: NICKEL (II) ION (NIb)
5c: NICKEL (II) ION (NIc)
5d: NICKEL (II) ION (NId)
5e: NICKEL (II) ION (NIe)
5f: NICKEL (II) ION (NIf)
5g: NICKEL (II) ION (NIg)
5h: NICKEL (II) ION (NIh)
5i: NICKEL (II) ION (NIi)
5j: NICKEL (II) ION (NIj)
5k: NICKEL (II) ION (NIk)
5l: NICKEL (II) ION (NIl)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
097
2
Ligand/Ion
(2S,3R)-N~4~-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N~1~,2-DIHYDROXY-3-(2-METHYLPROPYL)BUTANEDIAMIDE
2
CD
6
Ligand/Ion
CADMIUM ION
3
MG
6
Ligand/Ion
MAGNESIUM ION
4
NA
5
Ligand/Ion
SODIUM ION
5
NI
12
Ligand/Ion
NICKEL (II) ION
6
ZN
2
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
ASP A:368 , THR A:369 , LEU A:370 , GLY A:371 , HIS A:401 , GLU A:402 , HIS A:405 , HIS A:411 , ALA A:431 , SER A:432 , MET A:433 , LEU A:434 , ZN A:1553 , HOH A:2066 , HOH A:2122
BINDING SITE FOR RESIDUE 097 A1001
02
AC2
SOFTWARE
ASP B:368 , THR B:369 , LEU B:370 , GLY B:371 , HIS B:401 , GLU B:402 , HIS B:405 , HIS B:411 , ALA B:431 , SER B:432 , MET B:433 , LEU B:434 , ZN B:1554 , HOH B:2087 , HOH B:2088
BINDING SITE FOR RESIDUE 097 B1001
03
AC3
SOFTWARE
HIS A:401 , HIS A:405 , HIS A:411 , 097 A:1001
BINDING SITE FOR RESIDUE ZN A1553
04
AC4
SOFTWARE
HIS B:401 , HIS B:405 , HIS B:411 , 097 B:1001
BINDING SITE FOR RESIDUE ZN B1554
05
AC5
SOFTWARE
GLU A:261 , ASP A:344 , ASP A:465 , HOH A:2038 , HOH A:2081
BINDING SITE FOR RESIDUE CD A1554
06
AC6
SOFTWARE
GLU A:315 , GLU A:320 , HOH A:2023 , HOH A:2026
BINDING SITE FOR RESIDUE CD A1555
07
AC7
SOFTWARE
GLU A:494 , HIS B:313 , HOH B:2010 , HOH B:2022 , HOH B:2028
BINDING SITE FOR RESIDUE NI A1556
08
AC8
SOFTWARE
HIS A:280 , HOH A:2046 , ASP B:483
BINDING SITE FOR RESIDUE CD A1557
09
AC9
SOFTWARE
GLU A:261 , ASP A:344 , ASP A:351 , CYS A:462 , ASP A:465 , HOH A:2080
BINDING SITE FOR RESIDUE CD A1558
10
BC1
SOFTWARE
ASP A:483 , HOH A:2089 , HIS B:280
BINDING SITE FOR RESIDUE CD B1555
11
BC2
SOFTWARE
HIS A:313 , GLU B:494 , ASP B:495
BINDING SITE FOR RESIDUE NI B1556
12
BC3
SOFTWARE
GLU B:261 , ASP B:344 , ASP B:465 , HOH B:2026 , HOH B:2063
BINDING SITE FOR RESIDUE CD B1557
13
BC4
SOFTWARE
GLU B:261 , ASP B:344 , ASP B:351 , CYS B:462 , ASP B:465 , HOH B:2061
BINDING SITE FOR RESIDUE NI B1558
14
BC5
SOFTWARE
HIS A:313 , HOH A:2009 , GLU B:494
BINDING SITE FOR RESIDUE NI B1559
15
BC6
SOFTWARE
GLU A:320 , HOH A:2024 , HOH A:2025
BINDING SITE FOR RESIDUE NI A1559
16
BC7
SOFTWARE
HIS A:339 , HOH A:2035
BINDING SITE FOR RESIDUE MG A1560
17
BC8
SOFTWARE
HIS A:428 , HOH A:2064
BINDING SITE FOR RESIDUE NI A1561
18
BC9
SOFTWARE
GLU A:494 , ASP A:495 , HIS B:313
BINDING SITE FOR RESIDUE NI A1562
19
CC1
SOFTWARE
HIS A:498 , HOH A:2100
BINDING SITE FOR RESIDUE NI A1563
20
CC2
SOFTWARE
HIS A:525 , HOH A:2073 , HOH A:2104
BINDING SITE FOR RESIDUE NI A1564
21
CC3
SOFTWARE
HIS B:439 , ASP B:530 , ASN B:542
BINDING SITE FOR RESIDUE MG B1560
22
CC4
SOFTWARE
HIS B:428 , HOH B:2051
BINDING SITE FOR RESIDUE NI B1561
23
CC5
SOFTWARE
HIS B:459
BINDING SITE FOR RESIDUE MG B1562
24
CC6
SOFTWARE
HIS B:498
BINDING SITE FOR RESIDUE NI B1563
25
CC7
SOFTWARE
ASP A:360 , LEU A:361 , CYS A:367 , THR A:369 , GLU A:389 , NA A:1566
BINDING SITE FOR RESIDUE NA A1565
26
CC8
SOFTWARE
ASP A:360 , CYS A:367 , NA A:1565 , HOH A:2050
BINDING SITE FOR RESIDUE NA A1566
27
CC9
SOFTWARE
PRO A:410 , ASP A:412 , MET A:430 , SER A:447
BINDING SITE FOR RESIDUE NA A1567
28
DC1
SOFTWARE
ASP B:360 , LEU B:361 , CYS B:367 , ASP B:368 , THR B:369 , GLU B:389 , NA B:1565 , HOH B:2039
BINDING SITE FOR RESIDUE NA B1564
29
DC2
SOFTWARE
ASP B:360 , CYS B:367 , NA B:1564 , HOH B:2039
BINDING SITE FOR RESIDUE NA B1565
30
DC3
SOFTWARE
HIS A:439 , HOH A:2069
BINDING SITE FOR RESIDUE NI A1568
31
DC4
SOFTWARE
VAL A:518 , LEU A:519 , HIS B:525
BINDING SITE FOR RESIDUE MG A1569
32
DC5
SOFTWARE
HIS B:339
BINDING SITE FOR RESIDUE MG B1566
33
DC6
SOFTWARE
HIS B:439
BINDING SITE FOR RESIDUE MG B1567
[
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
(3, 6)
Info
All PROSITE Patterns/Profiles
1: ADAM_MEPRO (A:258-467,B:258-467)
2: ZINC_PROTEASE (A:398-407,B:398-407)
3: TSP1 (A:550-551,B:550-551|-|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADAM_MEPRO
PS50215
ADAM type metalloprotease domain profile.
ATS1_HUMAN
258-467
2
A:258-467
B:258-467
2
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
ATS1_HUMAN
398-407
2
A:398-407
B:398-407
3
TSP1
PS50092
Thrombospondin type-1 (TSP1) repeat profile.
ATS1_HUMAN
559-614
908-967
854-905
2
A:550-551
B:550-551
-
-
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.5 (A:256-359 | B:256-359)
Exon 1.6c (A:360-404 | B:360-404)
Exon 1.7d (A:404-460 (gaps) | B:404-460 (gaps...)
Exon 1.8a (A:460-548 (gaps) | B:460-548 (gaps...)
Exon 1.8d (A:549-551 | B:549-552)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.5
2: Boundary 1.5/1.6c
3: Boundary 1.6c/1.7d
4: Boundary 1.7d/1.8a
5: Boundary 1.8a/1.8d
6: Boundary 1.8d/1.9a
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
1.1
ENST00000284984
1
ENSE00001017374
chr21:
28217728-28216544
1185
ATS1_HUMAN
1-244
244
0
-
-
1.5
ENST00000284984
5
ENSE00001017377
chr21:
28215004-28214658
347
ATS1_HUMAN
244-359
116
2
A:256-359
B:256-359
104
104
1.6c
ENST00000284984
6c
ENSE00001017373
chr21:
28214309-28214177
133
ATS1_HUMAN
360-404
45
2
A:360-404
B:360-404
45
45
1.7d
ENST00000284984
7d
ENSE00001017382
chr21:
28213484-28213317
168
ATS1_HUMAN
404-460
57
2
A:404-460 (gaps)
B:404-460 (gaps)
57
57
1.8a
ENST00000284984
8a
ENSE00001017378
chr21:
28212881-28212595
287
ATS1_HUMAN
460-555
96
2
A:460-548 (gaps)
B:460-548 (gaps)
89
89
1.8d
ENST00000284984
8d
ENSE00001247753
chr21:
28212380-28212194
187
ATS1_HUMAN
556-618
63
2
A:549-551
B:549-552
3
4
1.9a
ENST00000284984
9a
ENSE00001017375
chr21:
28212081-28211906
176
ATS1_HUMAN
618-676
59
0
-
-
1.9c
ENST00000284984
9c
ENSE00001247815
chr21:
28210933-28210758
176
ATS1_HUMAN
677-735
59
0
-
-
1.10b
ENST00000284984
10b
ENSE00001923806
chr21:
28210597-28208606
1992
ATS1_HUMAN
735-967
233
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Reprolysin_2jihB01 (B:258-467)
1b: PFAM_Reprolysin_2jihB02 (B:258-467)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Reprolysin
(9)
Homo sapiens (Human)
(9)
1a
Reprolysin-2jihB01
B:258-467
1b
Reprolysin-2jihB02
B:258-467
[
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
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 (105 KB)
Header - Asym.Unit
Biol.Unit 1 (51 KB)
Header - Biol.Unit 1
Biol.Unit 2 (50 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
2JIH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help