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.
1T0L
Asym. Unit
Info
Asym.Unit (297 KB)
Biol.Unit 1 (148 KB)
Biol.Unit 2 (148 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 CYTOSOLIC NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH NADP, ISOCITRATE, AND CALCIUM(2+)
Authors
:
X. Xu, J. Zhao, B. Peng, Q. Huang, E. Arnold, J. Ding
Date
:
10 Apr 04 (Deposition) - 15 Jun 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.41
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Rossmann Fold, Nadp, Isocitrate, Calcium, Quaternary Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Xu, J. Zhao, Z. Xu, B. Peng, Q. Huang, E. Arnold, J. Ding
Structures Of Human Cytosolic Nadp-Dependent Isocitrate Dehydrogenase Reveal A Novel Self-Regulatory Mechanism Of Activity
J. Biol. Chem. V. 279 33946 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: ISOCITRIC ACID (ICTa)
2b: ISOCITRIC ACID (ICTb)
2c: ISOCITRIC ACID (ICTc)
2d: ISOCITRIC ACID (ICTd)
3a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
3b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
3c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
3d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
ICT
4
Ligand/Ion
ISOCITRIC ACID
3
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:109 , ASP A:275 , ASP A:279 , ICT A:1616 , HOH A:1763 , ASP B:252
BINDING SITE FOR RESIDUE CA A 1717
02
AC2
SOFTWARE
ASP A:252 , ASP B:275 , ASP B:279 , ICT B:1617 , HOH B:1897
BINDING SITE FOR RESIDUE CA B 1718
03
AC3
SOFTWARE
ASP C:275 , ASP C:279 , ICT C:1618 , HOH C:1733 , HOH C:1859 , ASP D:252
BINDING SITE FOR RESIDUE CA C 1719
04
AC4
SOFTWARE
ASP C:252 , ASP D:275 , ASP D:279 , ICT D:1619 , HOH D:1806 , HOH D:1815
BINDING SITE FOR RESIDUE CA D 1720
05
AC5
SOFTWARE
LYS A:72 , ALA A:74 , THR A:75 , ILE A:76 , THR A:77 , ARG A:82 , ASN A:96 , LEU A:288 , ALA A:308 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , THR A:327 , ASN A:328 , ICT A:1616 , HOH A:1718 , HOH A:1720 , HOH A:1773 , HOH A:1782 , HOH A:1807 , HOH A:1844 , HOH A:1856 , HOH A:1859 , HOH A:1914 , GLN B:257 , LYS B:260 , HOH B:1799
BINDING SITE FOR RESIDUE NAP A 1515
06
AC6
SOFTWARE
ASP A:253 , GLN A:257 , LYS A:260 , LYS B:72 , ALA B:74 , THR B:75 , ILE B:76 , THR B:77 , ARG B:82 , ASN B:96 , LEU B:288 , ALA B:308 , HIS B:309 , GLY B:310 , THR B:311 , VAL B:312 , THR B:313 , ARG B:314 , HIS B:315 , ASN B:328 , ICT B:1617 , HOH B:1721 , HOH B:1722 , HOH B:1737 , HOH B:1741 , HOH B:1749 , HOH B:1803 , HOH B:1872 , HOH B:1897
BINDING SITE FOR RESIDUE NAP B 1516
07
AC7
SOFTWARE
LYS C:72 , ALA C:74 , THR C:75 , ILE C:76 , THR C:77 , ARG C:82 , ASN C:96 , LEU C:288 , ALA C:308 , HIS C:309 , GLY C:310 , THR C:311 , VAL C:312 , THR C:313 , ARG C:314 , HIS C:315 , THR C:327 , ASN C:328 , ICT C:1618 , HOH C:1723 , HOH C:1727 , HOH C:1739 , HOH C:1743 , HOH C:1746 , HOH C:1793 , HOH C:1819 , HOH C:1852 , HOH C:1907 , ASP D:253 , GLN D:257 , LYS D:260
BINDING SITE FOR RESIDUE NAP C 1517
08
AC8
SOFTWARE
ASP C:253 , GLN C:257 , LYS C:260 , LYS D:72 , ALA D:74 , THR D:75 , ILE D:76 , THR D:77 , ARG D:82 , ASN D:96 , LEU D:288 , ALA D:307 , ALA D:308 , HIS D:309 , GLY D:310 , THR D:311 , VAL D:312 , THR D:313 , ARG D:314 , HIS D:315 , ASN D:328 , ICT D:1619 , HOH D:1748 , HOH D:1771 , HOH D:1825 , HOH D:1826 , HOH D:1922
BINDING SITE FOR RESIDUE NAP D 1518
09
AC9
SOFTWARE
THR A:77 , SER A:94 , ARG A:100 , ARG A:109 , ARG A:132 , TYR A:139 , ASP A:275 , NAP A:1515 , CA A:1717 , LYS B:212 , THR B:214 , ASP B:252 , HOH B:1886
BINDING SITE FOR RESIDUE ICT A 1616
10
BC1
SOFTWARE
LYS A:212 , THR A:214 , ASP A:252 , THR B:77 , SER B:94 , ARG B:100 , ARG B:109 , ARG B:132 , TYR B:139 , ASP B:275 , NAP B:1516 , CA B:1718
BINDING SITE FOR RESIDUE ICT B 1617
11
BC2
SOFTWARE
THR C:77 , SER C:94 , ARG C:100 , ARG C:109 , ARG C:132 , TYR C:139 , ASP C:275 , NAP C:1517 , CA C:1719 , LYS D:212 , THR D:214 , ILE D:215 , ASP D:252
BINDING SITE FOR RESIDUE ICT C 1618
12
BC3
SOFTWARE
LYS C:212 , THR C:214 , ASP C:252 , THR D:77 , SER D:94 , ARG D:100 , ARG D:109 , ARG D:132 , TYR D:139 , ASP D:275 , NAP D:1518 , CA D:1720 , HOH D:1767
BINDING SITE FOR RESIDUE ICT D 1619
[
close Site info
]
SAPs(SNPs)/Variants
(7, 28)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036013 (R132C, chain A/B/C/D, )
2: VAR_IDHC_HUMAN_CCDS2381_1_01 (R132C, chain A/B/C/D, )
3: VAR_055454 (R132G, chain A/B/C/D, )
4: VAR_055455 (R132H, chain A/B/C/D, )
5: VAR_055456 (R132L, chain A/B/C/D, )
6: VAR_055457 (R132S, chain A/B/C/D, )
7: VAR_049780 (V178I, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_036013
R
132
C
IDHC_HUMAN
Unclassified
---
A/B/C/D
R
132
C
2
CancerSNP
VAR_IDHC_HUMAN_CCDS2381_1_01
*
R
132
C
IDHC_HUMAN
Disease (Colorectal cancer)
---
A/B/C/D
R
132
C
3
UniProt
VAR_055454
R
132
G
IDHC_HUMAN
Unclassified
---
A/B/C/D
R
132
G
4
UniProt
VAR_055455
R
132
H
IDHC_HUMAN
Unclassified
---
A/B/C/D
R
132
H
5
UniProt
VAR_055456
R
132
L
IDHC_HUMAN
Unclassified
---
A/B/C/D
R
132
L
6
UniProt
VAR_055457
R
132
S
IDHC_HUMAN
Unclassified
---
A/B/C/D
R
132
S
7
UniProt
VAR_049780
V
178
I
IDHC_HUMAN
Polymorphism
34218846
A/B/C/D
V
178
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IDH_IMDH (A:271-290,B:271-290,C:271-290,D:27...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IDH_IMDH
PS00470
Isocitrate and isopropylmalate dehydrogenases signature.
IDHC_HUMAN
271-290
4
A:271-290
B:271-290
C:271-290
D:271-290
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.6a (A:1-41 | B:1-41 | C:1-41 | D:1-41)
Exon 1.7c (A:41-138 | B:41-138 | C:41-138 | D...)
Exon 1.8b (A:139-174 | B:139-174 | C:139-174 ...)
Exon 1.9b (A:174-233 | B:174-233 | C:174-233 ...)
Exon 1.10 (A:233-284 | B:233-284 | C:233-284 ...)
Exon 1.11b (A:284-331 | B:284-331 | C:284-331 ...)
Exon 1.12 (A:331-385 | B:331-385 | C:331-385 ...)
Exon 1.13f (A:385-414 | B:385-414 | C:385-414 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5d/1.6a
2: Boundary 1.6a/1.7c
3: Boundary 1.7c/1.8b
4: Boundary 1.8b/1.9b
5: Boundary 1.9b/1.10
6: Boundary 1.10/1.11b
7: Boundary 1.11b/1.12
8: Boundary 1.12/1.13f
9: Boundary 1.13f/-
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
1.3a
ENST00000345146
3a
ENSE00001908890
chr2:
209119857-209119663
195
IDHC_HUMAN
-
0
0
-
-
1.5d
ENST00000345146
5d
ENSE00001357891
chr2:
209118683-209118610
74
IDHC_HUMAN
-
0
0
-
-
1.6a
ENST00000345146
6a
ENSE00002149609
chr2:
209116291-209116154
138
IDHC_HUMAN
1-41
41
4
A:1-41
B:1-41
C:1-41
D:1-41
41
41
41
41
1.7c
ENST00000345146
7c
ENSE00000934687
chr2:
209113384-209113093
292
IDHC_HUMAN
41-138
98
4
A:41-138
B:41-138
C:41-138
D:41-138
98
98
98
98
1.8b
ENST00000345146
8b
ENSE00002162985
chr2:
209110148-209110043
106
IDHC_HUMAN
139-174
36
4
A:139-174
B:139-174
C:139-174
D:139-174
36
36
36
36
1.9b
ENST00000345146
9b
ENSE00001796387
chr2:
209108328-209108151
178
IDHC_HUMAN
174-233
60
4
A:174-233
B:174-233
C:174-233
D:174-233
60
60
60
60
1.10
ENST00000345146
10
ENSE00000934684
chr2:
209106869-209106718
152
IDHC_HUMAN
233-284
52
4
A:233-284
B:233-284
C:233-284
D:233-284
52
52
52
52
1.11b
ENST00000345146
11b
ENSE00000934683
chr2:
209104727-209104587
141
IDHC_HUMAN
284-331
48
4
A:284-331
B:284-331
C:284-331
D:284-331
48
48
48
48
1.12
ENST00000345146
12
ENSE00000934682
chr2:
209103957-209103795
163
IDHC_HUMAN
331-385
55
4
A:331-385
B:331-385
C:331-385
D:331-385
55
55
55
55
1.13f
ENST00000345146
13f
ENSE00000934681
chr2:
209101893-209100951
943
IDHC_HUMAN
385-414
30
4
A:385-414
B:385-414
C:385-414
D:385-414
30
30
30
30
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1t0la_ (A:)
1b: SCOP_d1t0lb_ (B:)
1c: SCOP_d1t0lc_ (C:)
1d: SCOP_d1t0ld_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Superfamily
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Family
:
Dimeric isocitrate & isopropylmalate dehydrogenases
(102)
Protein domain
:
NADP-dependent isocitrate dehydrogenase
(4)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1t0la_
A:
1b
d1t0lb_
B:
1c
d1t0lc_
C:
1d
d1t0ld_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1t0lA00 (A:1-414)
1b: CATH_1t0lB00 (B:1-414)
1c: CATH_1t0lC00 (C:1-414)
1d: CATH_1t0lD00 (D:1-414)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Isopropylmalate Dehydrogenase
(91)
Homologous Superfamily
:
Isopropylmalate Dehydrogenase
(91)
Human (Homo sapiens)
(3)
1a
1t0lA00
A:1-414
1b
1t0lB00
B:1-414
1c
1t0lC00
C:1-414
1d
1t0lD00
D:1-414
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Iso_dh_1t0lD01 (D:9-401)
1b: PFAM_Iso_dh_1t0lD02 (D:9-401)
1c: PFAM_Iso_dh_1t0lD03 (D:9-401)
1d: PFAM_Iso_dh_1t0lD04 (D:9-401)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Iso_DH
(49)
Family
:
Iso_dh
(38)
Homo sapiens (Human)
(5)
1a
Iso_dh-1t0lD01
D:9-401
1b
Iso_dh-1t0lD02
D:9-401
1c
Iso_dh-1t0lD03
D:9-401
1d
Iso_dh-1t0lD04
D:9-401
[
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 (297 KB)
Header - Asym.Unit
Biol.Unit 1 (148 KB)
Header - Biol.Unit 1
Biol.Unit 2 (148 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
1T0L
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help