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.
3RV5
Biol. Unit 5
Info
Asym.Unit (128 KB)
Biol.Unit 1 (32 KB)
Biol.Unit 2 (31 KB)
Biol.Unit 3 (32 KB)
Biol.Unit 4 (30 KB)
Biol.Unit 5 (221 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 CARDIAC TROPONIN C REGULATORY DOMAIN IN COMPLEX WITH CADMIUM AND DEOXYCHOLIC ACID
Authors
:
A. Y. Li, J. Lee, D. Borek, Z. Otwinowski, G. Tibbits, M. Paetzel
Date
:
06 May 11 (Deposition) - 31 Aug 11 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
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)
Biol. Unit 5: A,B,C,D (2x)
Keywords
:
Helix-Loop-Helix Ef-Hand Motif, Metal Ion Coordination, Calcium Sensor, Contractile Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Y. Li, J. Lee, D. Borek, Z. Otwinowski, G. F. Tibbits, M. Paetzel
Crystal Structure Of Cardiac Troponin C Regulatory Domain I Complex With Cadmium And Deoxycholic Acid Reveals Novel Conformation.
J. Mol. Biol. V. 413 699 2011
[
close entry info
]
Hetero Components
(2, 28)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
2c: CADMIUM ION (CDc)
2d: CADMIUM ION (CDd)
2e: CADMIUM ION (CDe)
2f: CADMIUM ION (CDf)
2g: CADMIUM ION (CDg)
2h: CADMIUM ION (CDh)
2i: CADMIUM ION (CDi)
2j: CADMIUM ION (CDj)
2k: CADMIUM ION (CDk)
2l: CADMIUM ION (CDl)
2m: CADMIUM ION (CDm)
2n: CADMIUM ION (CDn)
2o: CADMIUM ION (CDo)
2p: CADMIUM ION (CDp)
2q: CADMIUM ION (CDq)
2r: CADMIUM ION (CDr)
2s: CADMIUM ION (CDs)
2t: CADMIUM ION (CDt)
2u: CADMIUM ION (CDu)
3a: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDR... (DXCa)
3b: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDR... (DXCb)
3c: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDR... (DXCc)
3d: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDR... (DXCd)
3e: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDR... (DXCe)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CD
-1
Ligand/Ion
CADMIUM ION
3
DXC
6
Ligand/Ion
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
4
MSE
22
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(29, 29)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:30 , ASP A:33 , CYS A:35 , GLU A:40
BINDING SITE FOR RESIDUE CD A 101
02
AC2
SOFTWARE
GLU A:15 , GLU A:19 , CYS A:35 , HOH A:115 , HOH A:119
BINDING SITE FOR RESIDUE CD A 103
03
AC3
SOFTWARE
ASP A:65 , ASP A:67 , SER A:69 , THR A:71 , GLU A:76 , HOH A:110
BINDING SITE FOR RESIDUE CD A 102
04
AC4
SOFTWARE
ASP A:73 , ASP A:75 , HOH A:120 , HOH A:127 , HOH A:132
BINDING SITE FOR RESIDUE CD A 104
05
AC5
SOFTWARE
GLU A:66 , HOH A:140 , HOH C:123 , HOH C:138
BINDING SITE FOR RESIDUE CD A 105
06
AC6
SOFTWARE
LYS A:17 , PHE A:20 , GLU B:59 , VAL B:82 , CD B:106 , HOH B:135
BINDING SITE FOR RESIDUE DXC A 92
07
AC7
SOFTWARE
VAL A:79 , VAL A:82 , ARG A:83
BINDING SITE FOR RESIDUE DXC B 92
08
AC8
SOFTWARE
PHE A:27 , GLN A:50 , PHE A:77 , HOH A:135 , ILE C:4
BINDING SITE FOR RESIDUE DXC A 91
09
AC9
SOFTWARE
GLU B:66
BINDING SITE FOR RESIDUE CA B 109
10
BC1
SOFTWARE
GLU B:59 , GLU B:63 , HOH B:145
BINDING SITE FOR RESIDUE CA B 108
11
BC2
SOFTWARE
GLY B:30 , ASP B:33 , CYS B:35 , GLU B:40
BINDING SITE FOR RESIDUE CD B 101
12
BC3
SOFTWARE
ASP B:33 , CYS B:35 , HOH B:119 , HOH B:144 , HOH B:146 , HOH B:147 , HOH B:150
BINDING SITE FOR RESIDUE CD B 103
13
BC4
SOFTWARE
ASP B:65 , ASP B:67 , SER B:69 , THR B:71 , GLU B:76 , HOH B:110
BINDING SITE FOR RESIDUE CD B 102
14
BC5
SOFTWARE
ASP B:73 , ASP B:75 , HOH B:113 , HOH B:114 , HOH B:115 , HOH B:138
BINDING SITE FOR RESIDUE CD B 104
15
BC6
SOFTWARE
GLU B:32 , HOH B:142 , HOH B:148 , GLU C:15 , HOH C:138
BINDING SITE FOR RESIDUE CD B 105
16
BC7
SOFTWARE
DXC A:92 , GLU B:59 , HOH B:133 , HOH B:134 , HOH B:135
BINDING SITE FOR RESIDUE CD B 106
17
BC8
SOFTWARE
GLU A:14 , ASP B:62
BINDING SITE FOR RESIDUE CD B 107
18
BC9
SOFTWARE
GLY C:30 , ASP C:33 , CYS C:35 , GLU C:40
BINDING SITE FOR RESIDUE CD C 101
19
CC1
SOFTWARE
ASP C:33 , CYS C:35 , HOH C:111 , HOH C:116 , HOH C:133 , HOH C:143
BINDING SITE FOR RESIDUE CD C 103
20
CC2
SOFTWARE
ASP C:65 , ASP C:67 , SER C:69 , THR C:71 , GLU C:76 , HOH C:110
BINDING SITE FOR RESIDUE CD C 102
21
CC3
SOFTWARE
ASP C:73 , ASP C:75 , HOH C:113 , HOH C:119 , HOH C:130
BINDING SITE FOR RESIDUE CD C 104
22
CC4
SOFTWARE
GLU C:59 , GLU D:10 , DXC D:92
BINDING SITE FOR RESIDUE CD C 105
23
CC5
SOFTWARE
GLU C:32 , ASP D:75
BINDING SITE FOR RESIDUE CA C 106
24
CC6
SOFTWARE
PHE C:20 , LYS C:21 , PHE C:24 , HOH C:121 , VAL D:82
BINDING SITE FOR RESIDUE DXC C 92
25
CC7
SOFTWARE
GLY D:30 , ASP D:33 , CYS D:35 , GLU D:40
BINDING SITE FOR RESIDUE CD D 101
26
CC8
SOFTWARE
GLU D:15 , GLU D:19 , CYS D:35 , HOH D:128
BINDING SITE FOR RESIDUE CD D 103
27
CC9
SOFTWARE
ASP D:65 , ASP D:67 , SER D:69 , THR D:71 , GLU D:76 , HOH D:110
BINDING SITE FOR RESIDUE CD D 102
28
DC1
SOFTWARE
ASP D:73 , ASP D:75 , HOH D:118 , HOH D:120
BINDING SITE FOR RESIDUE CD D 104
29
DC2
SOFTWARE
TYR B:5 , GLU C:59 , VAL C:82 , CD C:105 , LYS D:17 , PHE D:24
BINDING SITE FOR RESIDUE DXC D 92
[
close Site info
]
SAPs(SNPs)/Variants
(3, 20)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_063070 (A8V, chain A/B/C/D, )
2: VAR_019776 (L29Q, chain A/B/C/D, )
3: VAR_063071 (C84Y, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_063070
A
8
V
TNNC1_HUMAN
Disease (CMH13)
---
A/B/C/D
A
8
V
2
UniProt
VAR_019776
L
29
Q
TNNC1_HUMAN
Disease (CMH13)
---
A/B/C/D
L
29
Q
3
UniProt
VAR_063071
C
84
Y
TNNC1_HUMAN
Disease (CMH13)
---
A/C
C
84
Y
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 24)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (A:33-51,B:33-51,C:33-51,A:52-85,B:...)
2: EF_HAND_1 (A:65-77,B:65-77,C:65-77,D:65-77|-|...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EF_HAND_2
PS50222
EF-hand calcium-binding domain profile.
TNNC1_HUMAN
33-51
52-87
92-127
128-161
16
A:33-51
B:33-51
C:33-51
D:33-51
A:52-85
B:52-82
C:52-85
D:52-82
-
-
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
TNNC1_HUMAN
65-77
105-117
141-153
8
A:65-77
B:65-77
C:65-77
D:65-77
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3rv5a_ (A:)
1b: SCOP_d3rv5b_ (B:)
1c: SCOP_d3rv5c_ (C:)
1d: SCOP_d3rv5d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
Calmodulin-like
(356)
Protein domain
:
Troponin C
(53)
Human (Homo sapiens), cardiac isoform [TaxId: 9606]
(16)
1a
d3rv5a_
A:
1b
d3rv5b_
B:
1c
d3rv5c_
C:
1d
d3rv5d_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain B
Chain C
Chain D
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
Asymmetric Unit 4
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 (128 KB)
Header - Asym.Unit
Biol.Unit 1 (32 KB)
Header - Biol.Unit 1
Biol.Unit 2 (31 KB)
Header - Biol.Unit 2
Biol.Unit 3 (32 KB)
Header - Biol.Unit 3
Biol.Unit 4 (30 KB)
Header - Biol.Unit 4
Biol.Unit 5 (221 KB)
Header - Biol.Unit 5
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
3RV5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help