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.
3K2B
Biol. Unit 3
Info
Asym.Unit (556 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (221 KB)
Biol.Unit 3 (228 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 PHOTOSYNTHETIC A4 ISOFORM GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE COMPLEXED WITH NAD, FROM ARABIDOPSIS THALIANA
Authors
:
S. Fermani, G. Falini, A. Thumiger, F. Sparla, L. Marri, P. Trost
Date
:
29 Sep 09 (Deposition) - 09 Jun 10 (Release) - 02 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,O,Q
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: O,Q (2x)
Keywords
:
Rossmann Fold, Calvin Cycle, Chloroplast, Membrane, Nadp, Oxidoreductase, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Fermani, F. Sparla, L. Marri, A. Thumiger, P. Pupillo, G. Falini, P. Trost
Structure Of Photosynthetic Glyceraldehyde-3-Phosphate Dehydrogenase (Isoform A4) From Arabidopsis Thaliana In Complex With Nad
Acta Crystallogr. , Sect. F V. 66 621 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 26)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
1e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
1g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
1h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
1i: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADi)
1j: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADj)
2a: SULFATE ION (SO4a)
2aa: SULFATE ION (SO4aa)
2ab: SULFATE ION (SO4ab)
2ac: SULFATE ION (SO4ac)
2ad: SULFATE ION (SO4ad)
2ae: SULFATE ION (SO4ae)
2af: SULFATE ION (SO4af)
2ag: SULFATE ION (SO4ag)
2ah: SULFATE ION (SO4ah)
2ai: SULFATE ION (SO4ai)
2aj: SULFATE ION (SO4aj)
2ak: SULFATE ION (SO4ak)
2al: SULFATE ION (SO4al)
2am: SULFATE ION (SO4am)
2an: SULFATE ION (SO4an)
2ao: SULFATE ION (SO4ao)
2ap: SULFATE ION (SO4ap)
2aq: SULFATE ION (SO4aq)
2ar: SULFATE ION (SO4ar)
2as: SULFATE ION (SO4as)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
2x: SULFATE ION (SO4x)
2y: SULFATE ION (SO4y)
2z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
SO4
22
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: EC7 (SOFTWARE)
02: EC8 (SOFTWARE)
03: EC9 (SOFTWARE)
04: FC1 (SOFTWARE)
05: FC2 (SOFTWARE)
06: FC3 (SOFTWARE)
07: FC4 (SOFTWARE)
08: FC5 (SOFTWARE)
09: FC6 (SOFTWARE)
10: FC7 (SOFTWARE)
11: FC8 (SOFTWARE)
12: FC9 (SOFTWARE)
13: GC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
EC7
SOFTWARE
GLY O:7 , PHE O:8 , GLY O:9 , ARG O:10 , ILE O:11 , ASP O:32 , THR O:33 , ARG O:77 , GLY O:95 , THR O:96 , GLY O:97 , PHE O:99 , THR O:119 , ALA O:120 , ASN O:313 , TYR O:317 , SO4 O:336 , HOH O:346 , HOH O:359 , HOH O:362 , HOH O:370 , HOH O:434 , HOH O:435 , HOH O:436 , HOH O:440
BINDING SITE FOR RESIDUE NAD O 335
02
EC8
SOFTWARE
HOH O:35 , THR O:179 , ASP O:181 , ARG O:195 , ARG O:231 , NAD O:335 , HOH O:398 , HOH O:415
BINDING SITE FOR RESIDUE SO4 O 336
03
EC9
SOFTWARE
SER O:148 , THR O:150 , THR O:208 , ALA O:210 , HOH O:397 , HOH O:407 , HOH O:857
BINDING SITE FOR RESIDUE SO4 O 337
04
FC1
SOFTWARE
GLY O:60A , GLU O:61 , THR O:62 , HOH O:375
BINDING SITE FOR RESIDUE SO4 O 334
05
FC2
SOFTWARE
ARG O:102 , LYS O:122A , GLY O:123 , ASP O:124
BINDING SITE FOR RESIDUE SO4 O 338
06
FC3
SOFTWARE
LYS C:122A , SER O:138 , HIS O:139 , ASP O:140 , LYS O:333 , HOH O:409
BINDING SITE FOR RESIDUE SO4 O 339
07
FC4
SOFTWARE
GLU O:253 , ASN O:256 , ARG O:260
BINDING SITE FOR RESIDUE SO4 O 340
08
FC5
SOFTWARE
GLY Q:7 , PHE Q:8 , GLY Q:9 , ARG Q:10 , ILE Q:11 , ASP Q:32 , THR Q:33 , ARG Q:77 , GLY Q:95 , THR Q:96 , GLY Q:97 , PHE Q:99 , THR Q:119 , ALA Q:120 , CYS Q:149 , THR Q:179 , ASN Q:313 , TYR Q:317 , SO4 Q:336 , HOH Q:346 , HOH Q:350 , HOH Q:446
BINDING SITE FOR RESIDUE NAD Q 335
09
FC6
SOFTWARE
THR Q:179 , ASP Q:181 , ARG Q:195 , ARG Q:231 , NAD Q:335
BINDING SITE FOR RESIDUE SO4 Q 336
10
FC7
SOFTWARE
SER Q:148 , THR Q:150 , THR Q:208 , GLY Q:209 , ALA Q:210 , HOH Q:467 , HOH Q:790
BINDING SITE FOR RESIDUE SO4 Q 337
11
FC8
SOFTWARE
PRO Q:126 , THR Q:127 , TYR Q:128 , ASN Q:133 , LEU Q:216 , HOH Q:462
BINDING SITE FOR RESIDUE SO4 Q 334
12
FC9
SOFTWARE
PHE Q:251 , ALA Q:252 , VAL Q:299 , HOH Q:477
BINDING SITE FOR RESIDUE SO4 Q 338
13
GC1
SOFTWARE
ARG Q:284 , HOH Q:805
BINDING SITE FOR RESIDUE SO4 Q 339
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (O:147-154,Q:147-154)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3PA1_ARATH
211-218
4
-
-
-
-
-
-
-
-
O:147-154
Q:147-154
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 20)
Info
all CATH domains
1a: CATH_3k2bA02 (A:148-313)
1b: CATH_3k2bC02 (C:148-313)
1c: CATH_3k2bD02 (D:148-313)
1d: CATH_3k2bE02 (E:148-313)
1e: CATH_3k2bF02 (F:148-313)
1f: CATH_3k2bG02 (G:148-313)
1g: CATH_3k2bH02 (H:148-313)
1h: CATH_3k2bO02 (O:148-313)
1i: CATH_3k2bQ02 (Q:148-313)
1j: CATH_3k2bB02 (B:148-313)
2a: CATH_3k2bA01 (A:1-147,A:314-333)
2b: CATH_3k2bO01 (O:1-147,O:314-333)
2c: CATH_3k2bQ01 (Q:1-147,Q:314-333)
2d: CATH_3k2bE01 (E:1-147,E:314-332)
2e: CATH_3k2bH01 (H:1-147,H:314-332)
2f: CATH_3k2bB01 (B:1-147,B:314-333)
2g: CATH_3k2bC01 (C:1-147,C:314-333)
2h: CATH_3k2bD01 (D:1-147,D:314-333)
2i: CATH_3k2bF01 (F:1-147,F:314-333)
2j: CATH_3k2bG01 (G:1-147,G:314-333)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Thale cress (Arabidopsis thaliana)
(3)
1a
3k2bA02
A:148-313
1b
3k2bC02
C:148-313
1c
3k2bD02
D:148-313
1d
3k2bE02
E:148-313
1e
3k2bF02
F:148-313
1f
3k2bG02
G:148-313
1g
3k2bH02
H:148-313
1h
3k2bO02
O:148-313
1i
3k2bQ02
Q:148-313
1j
3k2bB02
B:148-313
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Thale cress (Arabidopsis thaliana)
(15)
2a
3k2bA01
A:1-147,A:314-333
2b
3k2bO01
O:1-147,O:314-333
2c
3k2bQ01
Q:1-147,Q:314-333
2d
3k2bE01
E:1-147,E:314-332
2e
3k2bH01
H:1-147,H:314-332
2f
3k2bB01
B:1-147,B:314-333
2g
3k2bC01
C:1-147,C:314-333
2h
3k2bD01
D:1-147,D:314-333
2i
3k2bF01
F:1-147,F:314-333
2j
3k2bG01
G:1-147,G:314-333
[
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 O
Chain Q
Asymmetric Unit 1
Asymmetric Unit 2
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 (556 KB)
Header - Asym.Unit
Biol.Unit 1 (223 KB)
Header - Biol.Unit 1
Biol.Unit 2 (221 KB)
Header - Biol.Unit 2
Biol.Unit 3 (228 KB)
Header - Biol.Unit 3
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
3K2B
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help