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.
1L9M
Asym. Unit
Info
Asym.Unit (235 KB)
Biol.Unit 1 (230 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THREE-DIMENSIONAL STRUCTURE OF THE HUMAN TRANSGLUTAMINASE 3 ENZYME: BINDING OF CALCIUM IONS CHANGE STRUCTURE FOR ACTIVATION
Authors
:
B. Ahvazi
Date
:
26 Mar 02 (Deposition) - 29 May 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Activation, Calcium Binding, Transglutaminase, X-Ray Structure, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Ahvazi, H. C. Kim, S. H. Kee, Z. Nemes, P. M. Steinert
Three-Dimensional Structure Of The Human Transglutaminase 3 Enzyme: Binding Of Calcium Ions Changes Structure For Activation.
Embo J. V. 21 2055 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: BROMIDE ION (BRa)
1b: BROMIDE ION (BRb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BR
2
Ligand/Ion
BROMIDE ION
2
CA
2
Ligand/Ion
CALCIUM ION
3
CL
2
Ligand/Ion
CHLORIDE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:169 , ARG A:587 , ILE A:589 , ILE A:590
BINDING SITE FOR RESIDUE BR A 700
2
AC2
SOFTWARE
ASP A:183 , SER A:186
BINDING SITE FOR RESIDUE CL A 701
3
AC3
SOFTWARE
ALA A:221 , ASN A:224 , ASN A:226 , ASN A:229 , HOH A:977
BINDING SITE FOR RESIDUE CA A 702
4
AC4
SOFTWARE
ARG B:169 , ARG B:587 , ILE B:589 , ILE B:590 , HOH B:1093
BINDING SITE FOR RESIDUE BR B 703
5
AC5
SOFTWARE
ASP B:183 , SER B:186 , HOH B:773
BINDING SITE FOR RESIDUE CL B 704
6
AC6
SOFTWARE
ALA B:221 , ASN B:224 , SER B:225 , ASN B:226 , ASN B:229 , HOH B:1001
BINDING SITE FOR RESIDUE CA B 705
[
close Site info
]
SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_040067 (T12K, chain A/B, )
2: VAR_040068 (I162L, chain A/B, )
3: VAR_040069 (S248N, chain A/B, )
4: VAR_040070 (R561R, chain A/B, )
5: VAR_040071 (R653R, chain A/B, )
6: VAR_055360 (L686M, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_040067
T
13
K
TGM3_HUMAN
Polymorphism
214803
A/B
T
12
K
2
UniProt
VAR_040068
I
163
L
TGM3_HUMAN
Polymorphism
6048066
A/B
I
162
L
3
UniProt
VAR_040069
S
249
N
TGM3_HUMAN
Polymorphism
214814
A/B
S
248
N
4
UniProt
VAR_040070
K
562
R
TGM3_HUMAN
Polymorphism
1042617
A/B
R
561
R
5
UniProt
VAR_040071
G
654
R
TGM3_HUMAN
Polymorphism
214830
A/B
R
653
R
6
UniProt
VAR_055360
L
687
M
TGM3_HUMAN
Polymorphism
45581032
A/B
L
686
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: TRANSGLUTAMINASES (A:270-287,B:270-287)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRANSGLUTAMINASES
PS00547
Transglutaminases active site.
TGM3_HUMAN
271-288
2
A:270-287
B:270-287
[
close PROSITE info
]
Exons
(13, 26)
Info
All Exons
Exon 1.1b (A:1-2 | B:1-2)
Exon 1.2 (A:2-60 | B:2-60)
Exon 1.3 (A:60-140 | B:60-140)
Exon 1.4b (A:140-179 | B:140-179)
Exon 1.5a (A:180-222 | B:180-222)
Exon 1.6a (A:223-282 | B:223-282)
Exon 1.7 (A:282-327 | B:282-327)
Exon 1.8a (A:327-362 | B:327-362)
Exon 1.9 (A:362-444 | B:362-444)
Exon 1.10b (A:444-547 (gaps) | B:444-547 (gaps...)
Exon 1.12 (A:547-599 | B:547-599)
Exon 1.13 (A:600-644 | B:600-644)
Exon 1.14a (A:644-692 | B:644-692)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4b
05: Boundary 1.4b/1.5a
06: Boundary 1.5a/1.6a
07: Boundary 1.6a/1.7
08: Boundary 1.7/1.8a
09: Boundary 1.8a/1.9
10: Boundary 1.9/1.10b
11: Boundary 1.10b/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14a
14: Boundary 1.14a/-
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
1.1b
ENST00000381458
1b
ENSE00001884839
chr20:
2276647-2276716
70
TGM3_HUMAN
1-3
3
2
A:1-2
B:1-2
2
2
1.2
ENST00000381458
2
ENSE00000858628
chr20:
2290303-2290476
174
TGM3_HUMAN
3-61
59
2
A:2-60
B:2-60
59
59
1.3
ENST00000381458
3
ENSE00000655744
chr20:
2290824-2291063
240
TGM3_HUMAN
61-141
81
2
A:60-140
B:60-140
81
81
1.4b
ENST00000381458
4b
ENSE00000655746
chr20:
2291657-2291775
119
TGM3_HUMAN
141-180
40
2
A:140-179
B:140-179
40
40
1.5a
ENST00000381458
5a
ENSE00000655748
chr20:
2293544-2293672
129
TGM3_HUMAN
181-223
43
2
A:180-222
B:180-222
43
43
1.6a
ENST00000381458
6a
ENSE00000655870
chr20:
2297714-2297891
178
TGM3_HUMAN
224-283
60
2
A:223-282
B:223-282
60
60
1.7
ENST00000381458
7
ENSE00001764210
chr20:
2297996-2298131
136
TGM3_HUMAN
283-328
46
2
A:282-327
B:282-327
46
46
1.8a
ENST00000381458
8a
ENSE00001696552
chr20:
2306495-2306598
104
TGM3_HUMAN
328-363
36
2
A:327-362
B:327-362
36
36
1.9
ENST00000381458
9
ENSE00001632148
chr20:
2308766-2309011
246
TGM3_HUMAN
363-445
83
2
A:362-444
B:362-444
83
83
1.10b
ENST00000381458
10b
ENSE00001671589
chr20:
2312648-2312956
309
TGM3_HUMAN
445-548
104
2
A:444-547 (gaps)
B:444-547 (gaps)
104
104
1.12
ENST00000381458
12
ENSE00001761978
chr20:
2315762-2315919
158
TGM3_HUMAN
548-600
53
2
A:547-599
B:547-599
53
53
1.13
ENST00000381458
13
ENSE00001622482
chr20:
2320500-2320633
134
TGM3_HUMAN
601-645
45
2
A:600-644
B:600-644
45
45
1.14a
ENST00000381458
14a
ENSE00001609199
chr20:
2321080-2321724
645
TGM3_HUMAN
645-693
49
2
A:644-692
B:644-692
49
49
[
close EXON info
]
SCOP Domains
(3, 8)
Info
All SCOP Domains
1a: SCOP_d1l9ma1 (A:1-140)
1b: SCOP_d1l9mb1 (B:1-140)
2a: SCOP_d1l9ma2 (A:479-593)
2b: SCOP_d1l9ma3 (A:594-692)
2c: SCOP_d1l9mb2 (B:472-593)
2d: SCOP_d1l9mb3 (B:594-692)
3a: SCOP_d1l9ma4 (A:141-461)
3b: SCOP_d1l9mb4 (B:141-460)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
Transglutaminase N-terminal domain
(17)
Protein domain
:
Transglutaminase N-terminal domain
(17)
Human (Homo sapiens), TGase E3 [TaxId: 9606]
(5)
1a
d1l9ma1
A:1-140
1b
d1l9mb1
B:1-140
Superfamily
:
Transglutaminase, two C-terminal domains
(18)
Family
:
Transglutaminase, two C-terminal domains
(17)
Protein domain
:
Transglutaminase, two C-terminal domains
(17)
Human (Homo sapiens), TGase E3 [TaxId: 9606]
(5)
2a
d1l9ma2
A:479-593
2b
d1l9ma3
A:594-692
2c
d1l9mb2
B:472-593
2d
d1l9mb3
B:594-692
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Transglutaminase core
(22)
Protein domain
:
Transglutaminase catalytic domain
(17)
Human (Homo sapiens), TGase E3 [TaxId: 9606]
(5)
3a
d1l9ma4
A:141-461
3b
d1l9mb4
B:141-460
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1l9mA02 (A:143-479)
1b: CATH_1l9mB02 (B:143-477)
2a: CATH_1l9mA04 (A:595-691)
2b: CATH_1l9mB04 (B:595-691)
2c: CATH_1l9mA03 (A:480-594)
2d: CATH_1l9mB03 (B:478-594)
2e: CATH_1l9mA01 (A:1-142)
2f: CATH_1l9mB01 (B:1-142)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Coagulation Factor XIII; Chain A, domain 2
(19)
Homologous Superfamily
:
Coagulation Factor XIII, subunit A, domain 2
(19)
Human (Homo sapiens)
(18)
1a
1l9mA02
A:143-479
1b
1l9mB02
B:143-477
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1l9mA04
A:595-691
2b
1l9mB04
B:595-691
2c
1l9mA03
A:480-594
2d
1l9mB03
B:478-594
2e
1l9mA01
A:1-142
2f
1l9mB01
B:1-142
[
close CATH info
]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_Transglut_C_1l9mB01 (B:594-692)
1b: PFAM_Transglut_C_1l9mB02 (B:594-692)
1c: PFAM_Transglut_C_1l9mB03 (B:594-692)
1d: PFAM_Transglut_C_1l9mB04 (B:594-692)
2a: PFAM_Transglut_core_1l9mB05 (B:239-354)
2b: PFAM_Transglut_core_1l9mB06 (B:239-354)
3a: PFAM_Transglut_N_1l9mB07 (B:3-119)
3b: PFAM_Transglut_N_1l9mB08 (B:3-119)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
E-set
(290)
Family
:
Transglut_C
(8)
Homo sapiens (Human)
(8)
1a
Transglut_C-1l9mB01
B:594-692
1b
Transglut_C-1l9mB02
B:594-692
1c
Transglut_C-1l9mB03
B:594-692
1d
Transglut_C-1l9mB04
B:594-692
Clan
:
Peptidase_CA
(169)
Family
:
Transglut_core
(7)
Homo sapiens (Human)
(7)
2a
Transglut_core-1l9mB05
B:239-354
2b
Transglut_core-1l9mB06
B:239-354
Clan
:
no clan defined [family: Transglut_N]
(7)
Family
:
Transglut_N
(7)
Homo sapiens (Human)
(7)
3a
Transglut_N-1l9mB07
B:3-119
3b
Transglut_N-1l9mB08
B:3-119
[
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 (235 KB)
Header - Asym.Unit
Biol.Unit 1 (230 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
1L9M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
