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.
2D2I
Biol. Unit 2
Info
Asym.Unit (341 KB)
Biol.Unit 1 (227 KB)
Biol.Unit 2 (222 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 NADP-DEPENDENT GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM SYNECHOCOCCUS SP. COMPLEXED WITH NADP+
Authors
:
T. Kitatani, Y. Nakamura, K. Wada, T. Kinoshita, M. Tamoi, S. Shigeoka, T. Tada
Date
:
09 Sep 05 (Deposition) - 11 Jul 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,O,P,Q,R
Biol. Unit 1: A,B (2x)
Biol. Unit 2: O,P,Q,R (1x)
Keywords
:
Glyceraldehyde 3-Phosphate Dehydrogenase, Rossmann Fold, Protein-Nadp+ Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Kitatani, Y. Nakamura, K. Wada, T. Kinoshita, M. Tamoi, S. Shigeoka, T. Tada
Structure Of Nadp-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase From Synechococcus Pcc7942 Complexed With Nadp
Acta Crystallogr. , Sect. F V. 62 315 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
1b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
1c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
1d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
1e: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPe)
1f: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPf)
2a: SULFATE ION (SO4a)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC7 (SOFTWARE)
11: BC8 (SOFTWARE)
12: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
SER O:154 , THR O:156 , THR O:213 , GLY O:214 , ALA O:215 , HOH O:6456 , HOH O:6838
BINDING SITE FOR RESIDUE SO4 O 3339
02
AC6
SOFTWARE
THR O:185 , ASP O:187 , ARG O:200 , ARG O:236 , NAP O:3341 , HOH O:6389
BINDING SITE FOR RESIDUE SO4 O 3340
03
AC7
SOFTWARE
SER P:154 , THR P:213 , GLY P:214 , ALA P:215 , HOH P:6600 , HOH P:6717
BINDING SITE FOR RESIDUE SO4 P 4339
04
AC8
SOFTWARE
THR P:185 , ASP P:187 , ARG P:200 , ARG P:236 , NAP P:4341 , HOH P:6395 , HOH P:6653
BINDING SITE FOR RESIDUE SO4 P 4340
05
AC9
SOFTWARE
SER Q:154 , THR Q:213 , GLY Q:214 , ALA Q:215 , HOH Q:6486
BINDING SITE FOR RESIDUE SO4 Q 5339
06
BC1
SOFTWARE
THR Q:185 , ASP Q:187 , ARG Q:200 , ARG Q:236 , NAP Q:5341 , HOH Q:6852
BINDING SITE FOR RESIDUE SO4 Q 5340
07
BC2
SOFTWARE
SER R:154 , THR R:213 , GLY R:214 , ALA R:215 , HOH R:6737 , HOH R:6832
BINDING SITE FOR RESIDUE SO4 R 6339
08
BC3
SOFTWARE
THR R:185 , ASP R:187 , ARG R:200 , ARG R:236 , NAP R:6341 , HOH R:6497 , HOH R:6858
BINDING SITE FOR RESIDUE SO4 R 6340
09
BC6
SOFTWARE
GLY O:9 , PHE O:10 , GLY O:11 , ARG O:12 , ILE O:13 , THR O:37 , ARG O:80 , SER O:98 , THR O:99 , GLY O:100 , THR O:122 , ALA O:123 , CYS O:155 , THR O:185 , LEU O:186 , ASN O:318 , TYR O:322 , SO4 O:3340 , HOH O:6515 , HOH O:6540 , HOH O:6562 , HOH O:6660 , HOH O:6719 , HOH O:6749 , HOH O:6836 , SER R:194 , HOH R:6833
BINDING SITE FOR RESIDUE NAP O 3341
10
BC7
SOFTWARE
GLY P:9 , PHE P:10 , GLY P:11 , ARG P:12 , ILE P:13 , ASN P:35 , THR P:37 , ARG P:80 , SER P:98 , THR P:99 , GLY P:100 , THR P:122 , ALA P:123 , CYS P:155 , LEU P:186 , ASN P:318 , GLU P:319 , TYR P:322 , SO4 P:4340 , HOH P:6395 , HOH P:6578 , HOH P:6638 , HOH P:6653 , HOH P:6664 , HOH P:6876 , SER Q:194 , HOH Q:6709
BINDING SITE FOR RESIDUE NAP P 4341
11
BC8
SOFTWARE
SER P:194 , HOH P:6659 , GLY Q:9 , PHE Q:10 , GLY Q:11 , ARG Q:12 , ILE Q:13 , ASN Q:35 , THR Q:37 , ARG Q:80 , SER Q:98 , THR Q:99 , GLY Q:100 , THR Q:122 , ALA Q:123 , CYS Q:155 , LEU Q:186 , ASN Q:318 , GLU Q:319 , TYR Q:322 , SO4 Q:5340 , HOH Q:6457 , HOH Q:6470 , HOH Q:6552 , HOH Q:6752
BINDING SITE FOR RESIDUE NAP Q 5341
12
BC9
SOFTWARE
SER O:194 , GLY R:9 , GLY R:11 , ARG R:12 , ILE R:13 , ASN R:35 , THR R:37 , ARG R:80 , SER R:98 , THR R:99 , GLY R:100 , VAL R:101 , PHE R:102 , THR R:122 , ALA R:123 , CYS R:155 , LEU R:186 , ASN R:318 , GLU R:319 , TYR R:322 , SO4 R:6340 , HOH R:6637 , HOH R:6846
BINDING SITE FOR RESIDUE NAP R 6341
[
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
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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, 12)
Info
all CATH domains
1a: CATH_2d2iA02 (A:154-318)
1b: CATH_2d2iB02 (B:154-318)
1c: CATH_2d2iO02 (O:154-318)
1d: CATH_2d2iP02 (P:154-318)
1e: CATH_2d2iQ02 (Q:154-318)
1f: CATH_2d2iR02 (R:154-318)
2a: CATH_2d2iA01 (A:1-153,A:319-338)
2b: CATH_2d2iB01 (B:1-153,B:319-338)
2c: CATH_2d2iO01 (O:1-153,O:319-338)
2d: CATH_2d2iP01 (P:1-153,P:319-338)
2e: CATH_2d2iQ01 (Q:1-153,Q:319-338)
2f: CATH_2d2iR01 (R:1-153,R:319-338)
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)
Synechococcus sp.. Organism_taxid: 1131.
(1)
1a
2d2iA02
A:154-318
1b
2d2iB02
B:154-318
1c
2d2iO02
O:154-318
1d
2d2iP02
P:154-318
1e
2d2iQ02
Q:154-318
1f
2d2iR02
R:154-318
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Synechococcus sp.. Organism_taxid: 1131.
(1)
2a
2d2iA01
A:1-153,A:319-338
2b
2d2iB01
B:1-153,B:319-338
2c
2d2iO01
O:1-153,O:319-338
2d
2d2iP01
P:1-153,P:319-338
2e
2d2iQ01
Q:1-153,Q:319-338
2f
2d2iR01
R:1-153,R:319-338
[
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 P
Chain Q
Chain R
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 (341 KB)
Header - Asym.Unit
Biol.Unit 1 (227 KB)
Header - Biol.Unit 1
Biol.Unit 2 (222 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
2D2I
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
