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.
1Z2B
Asym. Unit
Info
Asym.Unit (259 KB)
Biol.Unit 1 (246 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TUBULIN-COLCHICINE-VINBLASTINE: STATHMIN-LIKE DOMAIN COMPLEX
Authors
:
B. Gigant, C. Wang, R. B. G. Ravelli, F. Roussi, M. O. Steinmetz, P. A. Cur A. Sobel, M. Knossow
Date
:
08 Mar 05 (Deposition) - 31 May 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
4.10
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Alpha-Tubulin, Beta-Tubulin, Colchicine, Gtpase, Microtubule, Stathmin, Tubulin, Vinblastine, Cell Cycle
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Gigant, C. Wang, R. B. Ravelli, F. Roussi, M. O. Steinmetz, P. A. Curmi, A. Sobel, M. Knossow
Structural Basis For The Regulation Of Tubulin By Vinblastine.
Nature V. 435 519 2005
[
close entry info
]
Hetero Components
(5, 9)
Info
All Hetero Components
1a: 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOX... (CN2a)
1b: 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOX... (CN2b)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
3a: GUANOSINE-5'-TRIPHOSPHATE (GTPa)
3b: GUANOSINE-5'-TRIPHOSPHATE (GTPb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)... (VLBa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CN2
2
Ligand/Ion
2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE
2
GDP
2
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
3
GTP
2
Ligand/Ion
GUANOSINE-5'-TRIPHOSPHATE
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
VLB
1
Ligand/Ion
(2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:99 , GLY A:144 , THR A:145 , GTP A:600
BINDING SITE FOR RESIDUE MG A 500
2
AC2
SOFTWARE
ALA C:99 , ASN C:101 , GLY C:144 , GTP C:601 , LYS D:254
BINDING SITE FOR RESIDUE MG C 501
3
AC3
SOFTWARE
GLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ASP A:69 , GLU A:71 , ASP A:98 , ALA A:99 , SER A:140 , GLY A:142 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , PRO A:173 , VAL A:177 , SER A:178 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , MG A:500 , LYS B:254
BINDING SITE FOR RESIDUE GTP A 600
4
AC4
SOFTWARE
GLY C:10 , GLN C:11 , ALA C:12 , ILE C:16 , ASP C:69 , GLU C:71 , ASP C:98 , ALA C:99 , SER C:140 , GLY C:142 , GLY C:143 , GLY C:144 , THR C:145 , GLY C:146 , ILE C:171 , PRO C:173 , VAL C:177 , SER C:178 , GLU C:183 , ASN C:206 , TYR C:224 , ASN C:228 , ILE C:231 , MG C:501 , LYS D:254
BINDING SITE FOR RESIDUE GTP C 601
5
AC5
SOFTWARE
GLY B:10 , GLN B:11 , CYS B:12 , ASN B:101 , SER B:140 , GLY B:142 , GLY B:144 , THR B:145 , GLY B:146 , PRO B:173 , SER B:178 , GLU B:183 , ASN B:206 , TYR B:224 , ASN B:228
BINDING SITE FOR RESIDUE GDP B 602
6
AC6
SOFTWARE
GLY D:10 , GLN D:11 , CYS D:12 , GLN D:15 , ASN D:101 , SER D:140 , GLY D:142 , GLY D:143 , GLY D:144 , THR D:145 , GLY D:146 , PRO D:173 , VAL D:177 , ASP D:179 , GLU D:183 , ASN D:206 , TYR D:224 , ASN D:228
BINDING SITE FOR RESIDUE GDP D 603
7
AC7
SOFTWARE
SER A:178 , THR A:179 , VAL A:181 , VAL B:238 , CYS B:241 , LEU B:242 , ALA B:250 , LEU B:255 , VAL B:315 , ALA B:316 , LYS B:352 , ILE B:378
BINDING SITE FOR RESIDUE CN2 B 700
8
AC8
SOFTWARE
SER C:178 , THR C:179 , ALA C:180 , VAL C:181 , VAL D:238 , CYS D:241 , LEU D:242 , ALA D:250 , LEU D:255 , ASN D:258 , MET D:259 , VAL D:315 , ALA D:316 , LYS D:352 , ILE D:378
BINDING SITE FOR RESIDUE CN2 D 701
9
AC9
SOFTWARE
PRO B:175 , LYS B:176 , VAL B:177 , ASP B:179 , TYR B:210 , THR B:221 , PRO B:222 , THR B:223 , TYR B:224 , PRO C:325 , ASN C:329 , PHE C:351 , VAL C:353 , ILE C:355
BINDING SITE FOR RESIDUE VLB C 800
[
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
(4, 7)
Info
All PROSITE Patterns/Profiles
1: STATHMIN_3 (E:5-141)
2: STATHMIN_1 (E:45-49)
3: STATHMIN_2 (E:73-82)
4: TUBULIN (B:142-148,D:142-148,A:142-148,C:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
STATHMIN_3
PS51663
Stathmin-like (SLD) domain profile.
STMN4_RAT
48-189
1
E:5-141
2
STATHMIN_1
PS00563
Stathmin family signature 1.
STMN4_RAT
84-93
1
E:45-49
3
STATHMIN_2
PS01041
Stathmin family signature 2.
STMN4_RAT
117-126
1
E:73-82
4
TUBULIN
PS00227
Tubulin subunits alpha, beta, and gamma signature.
TBB2B_BOVIN
140-146
2
B:142-148
D:142-148
TBA1D_BOVIN
142-148
2
A:142-148
C:142-148
[
close PROSITE info
]
Exons
(4, 8)
Info
All Exons
Exon 1.1 (B:2-19 | D:2-19)
Exon 1.2 (B:20-58 (gaps) | D:20-58 (gaps))
Exon 1.3 (B:58-95 | D:58-95)
Exon 1.4 (B:95-438 (gaps) | D:95-438 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/-
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
ENSBTAT00000005346
1
ENSBTAE00000067590
chr23:
51448815-51448966
152
TBB2B_BOVIN
1-19
19
2
B:2-19
D:2-19
18
18
1.2
ENSBTAT00000005346
2
ENSBTAE00000380542
chr23:
51449714-51449822
109
TBB2B_BOVIN
20-56
37
2
B:20-58 (gaps)
D:20-58 (gaps)
39
39
1.3
ENSBTAT00000005346
3
ENSBTAE00000419208
chr23:
51450093-51450203
111
TBB2B_BOVIN
56-93
38
2
B:58-95
D:58-95
38
38
1.4
ENSBTAT00000005346
4
ENSBTAE00000067601
chr23:
51450543-51451603
1061
TBB2B_BOVIN
93-445
353
2
B:95-438 (gaps)
D:95-438 (gaps)
344
344
[
close EXON info
]
SCOP Domains
(5, 9)
Info
All SCOP Domains
1a: SCOP_d1z2be1 (E:4-141)
2a: SCOP_d1z2ba2 (A:246-437)
2b: SCOP_d1z2bc2 (C:246-437)
3a: SCOP_d1z2bb2 (B:246-438)
3b: SCOP_d1z2bd2 (D:246-438)
4a: SCOP_d1z2ba1 (A:2-245)
4b: SCOP_d1z2bc1 (C:2-245)
5a: SCOP_d1z2bb1 (B:2-245)
5b: SCOP_d1z2bd1 (D:2-245)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Non-globular all-alpha subunits of globular proteins
(135)
Superfamily
:
Stathmin
(21)
Family
:
Stathmin
(21)
Protein domain
:
Stathmin 4
(21)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(21)
1a
d1z2be1
E:4-141
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Bacillus chorismate mutase-like
(324)
Superfamily
:
Tubulin C-terminal domain-like
(76)
Family
:
Tubulin, C-terminal domain
(69)
Protein domain
:
Tubulin alpha-subunit
(10)
Cow (Bos taurus) [TaxId: 9913]
(5)
2a
d1z2ba2
A:246-437
2b
d1z2bc2
C:246-437
Protein domain
:
Tubulin beta-subunit
(8)
Cow (Bos taurus) [TaxId: 9913]
(5)
3a
d1z2bb2
B:246-438
3b
d1z2bd2
D:246-438
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Tubulin nucleotide-binding domain-like
(75)
Superfamily
:
Tubulin nucleotide-binding domain-like
(75)
Family
:
Tubulin, GTPase domain
(69)
Protein domain
:
Tubulin alpha-subunit
(9)
Cow (Bos taurus) [TaxId: 9913]
(4)
4a
d1z2ba1
A:2-245
4b
d1z2bc1
C:2-245
Protein domain
:
Tubulin beta-subunit
(8)
Cow (Bos taurus) [TaxId: 9913]
(5)
5a
d1z2bb1
B:2-245
5b
d1z2bd1
D:2-245
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 5)
Info
all PFAM domains
1a: PFAM_Tubulin_1z2bD01 (D:3-226)
1b: PFAM_Tubulin_1z2bD02 (D:3-226)
2a: PFAM_Tubulin_C_1z2bD03 (D:263-393)
2b: PFAM_Tubulin_C_1z2bD04 (D:263-393)
3a: PFAM_Stathmin_1z2bE01 (E:5-141)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Tubulin-like
(34)
Family
:
Tubulin
(34)
Bos taurus (Bovine)
(7)
1a
Tubulin-1z2bD01
D:3-226
1b
Tubulin-1z2bD02
D:3-226
Family
:
Tubulin_C
(11)
Bos taurus (Bovine)
(7)
2a
Tubulin_C-1z2bD03
D:263-393
2b
Tubulin_C-1z2bD04
D:263-393
Clan
:
no clan defined [family: Stathmin]
(4)
Family
:
Stathmin
(4)
Rattus norvegicus (Rat)
(4)
3a
Stathmin-1z2bE01
E:5-141
[
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
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 (259 KB)
Header - Asym.Unit
Biol.Unit 1 (246 KB)
Header - Biol.Unit 1
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
1Z2B
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help