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.
PLEASE WAIT...
Getting 'Exon' information from database.
2XF8
Asym. Unit
Info
Asym.Unit (809 KB)
Biol.Unit 1 (210 KB)
Biol.Unit 2 (209 KB)
Biol.Unit 3 (209 KB)
Biol.Unit 4 (207 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE FROM E.COLI IN COMPLEX WITH A NAD COFACTOR ANALOG (3-CHLOROACETYL ADENINE PYRIDINE DINUCLEOTIDE) AND SULFATE ANION
Authors
:
S. Moniot, C. Didierjean, S. Boschi-Muller, G. Branlant, C. Corbier
Date
:
20 May 10 (Deposition) - 08 Jun 11 (Release) - 15 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.95
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: E,F,G,H (1x)
Biol. Unit 2: A,B,C,D (1x)
Biol. Unit 3: M,N,O,P (1x)
Biol. Unit 4: I,J,K,L (1x)
Keywords
:
Aldehyde Dehydrogenase, Hydride Transfer, Cofactor Analog, Pyridoxal Phophate Biosynthesis, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Moniot, C. Didierjean, S. Boschi-Muller, G. Branlant, C. Corbier
Structural Characterization Of Erythrose-4- Phosphate Dehydrogenase From Escherichia Coli: Peculiar Features When Compared To Phosphorylating Gapdhs
To Be Published
[
close entry info
]
Hetero Components
(2, 24)
Info
All Hetero Components
1a: 3-(CHLOROACETYL) PYRIDINE ADENINED... (3CDa)
1b: 3-(CHLOROACETYL) PYRIDINE ADENINED... (3CDb)
1c: 3-(CHLOROACETYL) PYRIDINE ADENINED... (3CDc)
1d: 3-(CHLOROACETYL) PYRIDINE ADENINED... (3CDd)
1e: 3-(CHLOROACETYL) PYRIDINE ADENINED... (3CDe)
1f: 3-(CHLOROACETYL) PYRIDINE ADENINED... (3CDf)
1g: 3-(CHLOROACETYL) PYRIDINE ADENINED... (3CDg)
1h: 3-(CHLOROACETYL) PYRIDINE ADENINED... (3CDh)
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)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3CD
8
Ligand/Ion
3-(CHLOROACETYL) PYRIDINE ADENINEDINUCLEOTIDE
2
SO4
16
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:150 , HIS A:176 , THR A:208 , LYS A:209 , LEU A:210
BINDING SITE FOR RESIDUE SO4 A 500
02
AC2
SOFTWARE
GLY A:7 , PHE A:8 , GLY A:9 , ARG A:10 , ILE A:11 , ASN A:31 , GLU A:32 , LEU A:33 , GLU A:76 , ARG A:77 , GLY A:97 , TYR A:99 , SER A:119 , HIS A:120 , CYS A:149 , ASN A:313 , PHE A:317 , HOH A:2013 , HOH A:2014 , HOH A:2015 , ARG F:61
BINDING SITE FOR RESIDUE 3CD A 600
03
AC3
SOFTWARE
THR B:150 , HIS B:176 , THR B:208 , LYS B:209
BINDING SITE FOR RESIDUE SO4 B 500
04
AC4
SOFTWARE
SER C:148 , THR C:150 , HIS C:176 , THR C:208 , LYS C:209
BINDING SITE FOR RESIDUE SO4 C 500
05
AC5
SOFTWARE
GLY C:7 , GLY C:9 , ARG C:10 , ILE C:11 , ASN C:31 , GLU C:32 , LEU C:33 , CYS C:95 , GLY C:97 , TYR C:99 , SER C:119 , HIS C:120 , CYS C:149 , PHE C:317 , GLN H:63
BINDING SITE FOR RESIDUE 3CD C 600
06
AC6
SOFTWARE
THR D:150 , HIS D:176 , THR D:208 , LYS D:209
BINDING SITE FOR RESIDUE SO4 D 500
07
AC7
SOFTWARE
THR E:150 , THR E:208 , LYS E:209 , LEU E:210
BINDING SITE FOR RESIDUE SO4 E 500
08
AC8
SOFTWARE
ARG B:61 , GLY E:7 , GLY E:9 , ARG E:10 , ILE E:11 , ASN E:31 , GLU E:32 , ARG E:77 , CYS E:95 , THR E:96 , GLY E:97 , TYR E:99 , SER E:119 , HIS E:120 , SER E:148 , CYS E:149 , PHE E:317
BINDING SITE FOR RESIDUE 3CD E 600
09
AC9
SOFTWARE
THR F:150 , HIS F:176 , THR F:208 , LYS F:209
BINDING SITE FOR RESIDUE SO4 F 500
10
BC1
SOFTWARE
THR G:150 , HIS G:176 , THR G:208 , LYS G:209 , LEU G:210
BINDING SITE FOR RESIDUE SO4 G 500
11
BC2
SOFTWARE
ARG D:61 , GLY G:7 , GLY G:9 , ARG G:10 , ILE G:11 , ASN G:31 , GLU G:32 , LEU G:33 , CYS G:95 , GLY G:97 , TYR G:99 , SER G:119 , HIS G:120 , CYS G:149 , ASN G:313
BINDING SITE FOR RESIDUE 3CD G 600
12
BC3
SOFTWARE
SER H:148 , THR H:150 , HIS H:176 , THR H:208 , LYS H:209
BINDING SITE FOR RESIDUE SO4 H 500
13
BC4
SOFTWARE
THR I:150 , HIS I:176 , THR I:208 , LYS I:209 , LEU I:210
BINDING SITE FOR RESIDUE SO4 I 500
14
BC5
SOFTWARE
GLY I:7 , GLY I:9 , ARG I:10 , ILE I:11 , ASN I:31 , GLU I:32 , LEU I:33 , GLU I:76 , ARG I:77 , CYS I:95 , GLY I:97 , TYR I:99 , SER I:119 , HIS I:120 , SER I:148 , CYS I:149 , ASN I:313 , HOH I:2006
BINDING SITE FOR RESIDUE 3CD I 600
15
BC6
SOFTWARE
THR J:150 , HIS J:176 , THR J:208 , LYS J:209 , LEU J:210
BINDING SITE FOR RESIDUE SO4 J 500
16
BC7
SOFTWARE
THR K:150 , HIS K:176 , THR K:208 , LYS K:209
BINDING SITE FOR RESIDUE SO4 K 500
17
BC8
SOFTWARE
GLY K:7 , PHE K:8 , GLY K:9 , ARG K:10 , ILE K:11 , ASN K:31 , GLU K:32 , LEU K:33 , CYS K:95 , THR K:96 , GLY K:97 , TYR K:99 , SER K:119 , SER K:148 , CYS K:149 , PHE K:317 , GLN P:63 , ALA P:70
BINDING SITE FOR RESIDUE 3CD K 600
18
BC9
SOFTWARE
THR L:150 , HIS L:176 , THR L:208 , LYS L:209
BINDING SITE FOR RESIDUE SO4 L 500
19
CC1
SOFTWARE
THR M:150 , HIS M:176 , THR M:208 , LYS M:209 , LEU M:210
BINDING SITE FOR RESIDUE SO4 M 500
20
CC2
SOFTWARE
GLY M:7 , GLY M:9 , ARG M:10 , ILE M:11 , ASN M:31 , GLU M:32 , ARG M:77 , GLY M:97 , TYR M:99 , SER M:119 , HIS M:120 , CYS M:149 , ASN M:313 , PHE M:317
BINDING SITE FOR RESIDUE 3CD M 600
21
CC3
SOFTWARE
THR N:150 , HIS N:176 , THR N:208 , LYS N:209 , LEU N:210
BINDING SITE FOR RESIDUE SO4 N 500
22
CC4
SOFTWARE
THR O:150 , HIS O:176 , THR O:208 , LYS O:209 , LEU O:210
BINDING SITE FOR RESIDUE SO4 O 500
23
CC5
SOFTWARE
GLY O:7 , GLY O:9 , ARG O:10 , ILE O:11 , ASN O:31 , GLU O:32 , LEU O:33 , CYS O:95 , THR O:96 , GLY O:97 , SER O:119 , CYS O:149 , ASN O:313 , PHE O:317
BINDING SITE FOR RESIDUE 3CD O 600
24
CC6
SOFTWARE
THR P:150 , HIS P:176 , THR P:208 , LYS P:209 , LEU P:210
BINDING SITE FOR RESIDUE SO4 P 500
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 16)
Info
All PROSITE Patterns/Profiles
1: GAPDH (A:147-154,B:147-154,C:147-154,D:14...)
;
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.
E4PD_ECOLI
153-160
16
A:147-154
B:147-154
C:147-154
D:147-154
E:147-154
F:147-154
G:147-154
H:147-154
I:147-154
J:147-154
K:147-154
L:147-154
M:147-154
N:147-154
O:147-154
P: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.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 32)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_2xf8P01 (P:154-311)
1b: PFAM_Gp_dh_C_2xf8P02 (P:154-311)
1c: PFAM_Gp_dh_C_2xf8P03 (P:154-311)
1d: PFAM_Gp_dh_C_2xf8P04 (P:154-311)
1e: PFAM_Gp_dh_C_2xf8P05 (P:154-311)
1f: PFAM_Gp_dh_C_2xf8P06 (P:154-311)
1g: PFAM_Gp_dh_C_2xf8P07 (P:154-311)
1h: PFAM_Gp_dh_C_2xf8P08 (P:154-311)
1i: PFAM_Gp_dh_C_2xf8P09 (P:154-311)
1j: PFAM_Gp_dh_C_2xf8P10 (P:154-311)
1k: PFAM_Gp_dh_C_2xf8P11 (P:154-311)
1l: PFAM_Gp_dh_C_2xf8P12 (P:154-311)
1m: PFAM_Gp_dh_C_2xf8P13 (P:154-311)
1n: PFAM_Gp_dh_C_2xf8P14 (P:154-311)
1o: PFAM_Gp_dh_C_2xf8P15 (P:154-311)
1p: PFAM_Gp_dh_C_2xf8P16 (P:154-311)
2a: PFAM_Gp_dh_N_2xf8P17 (P:1-149)
2b: PFAM_Gp_dh_N_2xf8P18 (P:1-149)
2c: PFAM_Gp_dh_N_2xf8P19 (P:1-149)
2d: PFAM_Gp_dh_N_2xf8P20 (P:1-149)
2e: PFAM_Gp_dh_N_2xf8P21 (P:1-149)
2f: PFAM_Gp_dh_N_2xf8P22 (P:1-149)
2g: PFAM_Gp_dh_N_2xf8P23 (P:1-149)
2h: PFAM_Gp_dh_N_2xf8P24 (P:1-149)
2i: PFAM_Gp_dh_N_2xf8P25 (P:1-149)
2j: PFAM_Gp_dh_N_2xf8P26 (P:1-149)
2k: PFAM_Gp_dh_N_2xf8P27 (P:1-149)
2l: PFAM_Gp_dh_N_2xf8P28 (P:1-149)
2m: PFAM_Gp_dh_N_2xf8P29 (P:1-149)
2n: PFAM_Gp_dh_N_2xf8P30 (P:1-149)
2o: PFAM_Gp_dh_N_2xf8P31 (P:1-149)
2p: PFAM_Gp_dh_N_2xf8P32 (P:1-149)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Escherichia coli (strain K12)
(5)
1a
Gp_dh_C-2xf8P01
P:154-311
1b
Gp_dh_C-2xf8P02
P:154-311
1c
Gp_dh_C-2xf8P03
P:154-311
1d
Gp_dh_C-2xf8P04
P:154-311
1e
Gp_dh_C-2xf8P05
P:154-311
1f
Gp_dh_C-2xf8P06
P:154-311
1g
Gp_dh_C-2xf8P07
P:154-311
1h
Gp_dh_C-2xf8P08
P:154-311
1i
Gp_dh_C-2xf8P09
P:154-311
1j
Gp_dh_C-2xf8P10
P:154-311
1k
Gp_dh_C-2xf8P11
P:154-311
1l
Gp_dh_C-2xf8P12
P:154-311
1m
Gp_dh_C-2xf8P13
P:154-311
1n
Gp_dh_C-2xf8P14
P:154-311
1o
Gp_dh_C-2xf8P15
P:154-311
1p
Gp_dh_C-2xf8P16
P:154-311
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Escherichia coli (strain K12)
(5)
2a
Gp_dh_N-2xf8P17
P:1-149
2b
Gp_dh_N-2xf8P18
P:1-149
2c
Gp_dh_N-2xf8P19
P:1-149
2d
Gp_dh_N-2xf8P20
P:1-149
2e
Gp_dh_N-2xf8P21
P:1-149
2f
Gp_dh_N-2xf8P22
P:1-149
2g
Gp_dh_N-2xf8P23
P:1-149
2h
Gp_dh_N-2xf8P24
P:1-149
2i
Gp_dh_N-2xf8P25
P:1-149
2j
Gp_dh_N-2xf8P26
P:1-149
2k
Gp_dh_N-2xf8P27
P:1-149
2l
Gp_dh_N-2xf8P28
P:1-149
2m
Gp_dh_N-2xf8P29
P:1-149
2n
Gp_dh_N-2xf8P30
P:1-149
2o
Gp_dh_N-2xf8P31
P:1-149
2p
Gp_dh_N-2xf8P32
P:1-149
[
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
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
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 (809 KB)
Header - Asym.Unit
Biol.Unit 1 (210 KB)
Header - Biol.Unit 1
Biol.Unit 2 (209 KB)
Header - Biol.Unit 2
Biol.Unit 3 (209 KB)
Header - Biol.Unit 3
Biol.Unit 4 (207 KB)
Header - Biol.Unit 4
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
2XF8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
