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3CMC
Asym. Unit
Info
Asym.Unit (262 KB)
Biol.Unit 1 (254 KB)
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(1)
Title
:
THIOACYLENZYME INTERMEDIATE OF BACILLUS STEAROTHERMOPHILUS PHOSPHORYLATING GAPDH
Authors
:
S. Moniot, C. Vonrhein, G. Bricogne, C. Didierjean, C. Corbier
Date
:
21 Mar 08 (Deposition) - 17 Jun 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : O,P,Q,R
Biol. Unit 1: O,P,Q,R (1x)
Keywords
:
Microspectrophotometry, Reaction Intermediate, Dehydrogenase, Phosphate Binding Site, Thioacylenzyme, Glycolysis, Nad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Moniot, S. Bruno, C. Vonrhein, C. Didierjean, S. Boschi-Muller, M. Vas, G. Bricogne, G. Branlant, A. Mozzarelli, C. Corbier
Trapping Of The Thioacylglyceraldehyde-3-Phosphate Dehydrogenase Intermediate From Bacillus Stearothermophilus Direct Evidence For A Flip-Flop Mechanism
J. Biol. Chem. V. 283 21693 2008
[
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Hetero Components
(5, 35)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
2a: GLYCERALDEHYDE-3-PHOSPHATE (G3Ha)
2b: GLYCERALDEHYDE-3-PHOSPHATE (G3Hb)
2c: GLYCERALDEHYDE-3-PHOSPHATE (G3Hc)
2d: GLYCERALDEHYDE-3-PHOSPHATE (G3Hd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
4d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
5l: SULFATE ION (SO4l)
5m: SULFATE ION (SO4m)
5n: SULFATE ION (SO4n)
5o: SULFATE ION (SO4o)
5p: SULFATE ION (SO4p)
5q: SULFATE ION (SO4q)
5r: SULFATE ION (SO4r)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
2
G3H
4
Ligand/Ion
GLYCERALDEHYDE-3-PHOSPHATE
3
GOL
8
Ligand/Ion
GLYCEROL
4
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5
SO4
18
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER O:148 , THR O:207 , THR O:208 , GLY O:209 , ALA O:210
BINDING SITE FOR RESIDUE SO4 O 401
02
AC2
SOFTWARE
PRO P:121 , SER P:148 , THR P:207 , THR P:208 , GLY P:209 , ALA P:210
BINDING SITE FOR RESIDUE SO4 P 401
03
AC3
SOFTWARE
PRO Q:121 , SER Q:148 , THR Q:207 , THR Q:208 , GLY Q:209 , ALA Q:210
BINDING SITE FOR RESIDUE SO4 Q 401
04
AC4
SOFTWARE
SER R:148 , THR R:207 , THR R:208 , GLY R:209 , ALA R:210
BINDING SITE FOR RESIDUE SO4 R 401
05
AC5
SOFTWARE
THR O:179 , ASP O:181 , ARG O:195 , ARG O:231
BINDING SITE FOR RESIDUE SO4 O 402
06
AC6
SOFTWARE
THR P:179 , ASP P:181 , ARG P:195 , ARG P:231
BINDING SITE FOR RESIDUE SO4 P 402
07
AC7
SOFTWARE
THR Q:179 , ASP Q:181 , ARG Q:195 , ARG Q:231
BINDING SITE FOR RESIDUE SO4 Q 402
08
AC8
SOFTWARE
THR R:179 , ASP R:181 , ARG R:195 , ARG R:231
BINDING SITE FOR RESIDUE SO4 R 402
09
AC9
SOFTWARE
ARG O:169 , LYS P:303
BINDING SITE FOR RESIDUE SO4 O 403
10
BC1
SOFTWARE
ARG O:183 , HIS O:190 , LYS O:191
BINDING SITE FOR RESIDUE SO4 O 404
11
BC2
SOFTWARE
LYS Q:303 , ARG R:169
BINDING SITE FOR RESIDUE SO4 R 403
12
BC3
SOFTWARE
ARG Q:183 , PRO Q:188 , HIS Q:190 , LYS Q:191
BINDING SITE FOR RESIDUE SO4 Q 403
13
BC4
SOFTWARE
ARG R:52
BINDING SITE FOR RESIDUE SO4 R 404
14
BC5
SOFTWARE
SER R:58
BINDING SITE FOR RESIDUE SO4 R 405
15
BC6
SOFTWARE
ASN O:62 , ASN O:63
BINDING SITE FOR RESIDUE SO4 O 405
16
BC7
SOFTWARE
ARG R:183 , HIS R:190 , LYS R:191
BINDING SITE FOR RESIDUE SO4 R 406
17
BC8
SOFTWARE
ASP P:138 , LYS P:139 , LEU R:109 , GLY R:112 , ALA R:113 , LYS R:114
BINDING SITE FOR RESIDUE SO4 R 407
18
BC9
SOFTWARE
GLY O:85 , ALA O:111 , GLY O:112
BINDING SITE FOR RESIDUE SO4 O 406
19
CC1
SOFTWARE
SER O:148 , CYS O:149 , THR O:150 , HIS O:176 , THR O:179 , THR O:208 , GLY O:209 , ARG O:231
BINDING SITE FOR RESIDUE G3H O 400
20
CC2
SOFTWARE
SER P:148 , CYS P:149 , THR P:150 , HIS P:176 , THR P:208 , GLY P:209 , ARG P:231
BINDING SITE FOR RESIDUE G3H P 400
21
CC3
SOFTWARE
SER Q:148 , CYS Q:149 , THR Q:150 , HIS Q:176 , THR Q:179 , THR Q:208 , GLY Q:209 , ARG Q:231
BINDING SITE FOR RESIDUE G3H Q 400
22
CC4
SOFTWARE
SER R:148 , CYS R:149 , THR R:150 , HIS R:176 , THR R:179 , THR R:208 , GLY R:209 , ARG R:231
BINDING SITE FOR RESIDUE G3H R 400
23
CC5
SOFTWARE
GLY O:7 , GLY O:9 , ARG O:10 , ILE O:11 , ASN O:31 , ASP O:32 , LEU O:33 , ARG O:77 , SER O:95 , THR O:96 , GLY O:97 , ARG O:98 , PHE O:99 , SER O:119 , ALA O:120 , ASN O:180 , ASN O:313 , TYR O:317 , LEU R:187
BINDING SITE FOR RESIDUE NAD O 407
24
CC6
SOFTWARE
GLY P:7 , GLY P:9 , ARG P:10 , ILE P:11 , ASN P:31 , ASP P:32 , LEU P:33 , ARG P:77 , SER P:95 , THR P:96 , GLY P:97 , SER P:119 , ALA P:120 , ASN P:180 , ASN P:313 , TYR P:317
BINDING SITE FOR RESIDUE NAD P 403
25
CC7
SOFTWARE
GLY Q:7 , GLY Q:9 , ARG Q:10 , ILE Q:11 , ASN Q:31 , ASP Q:32 , LEU Q:33 , ARG Q:77 , SER Q:95 , THR Q:96 , GLY Q:97 , ARG Q:98 , PHE Q:99 , SER Q:119 , ALA Q:120 , ASN Q:180 , ASN Q:313 , TYR Q:317
BINDING SITE FOR RESIDUE NAD Q 404
26
CC8
SOFTWARE
GLY R:7 , GLY R:9 , ARG R:10 , ILE R:11 , ASN R:31 , ASP R:32 , LEU R:33 , ARG R:77 , SER R:95 , THR R:96 , GLY R:97 , ARG R:98 , PHE R:99 , SER R:119 , ALA R:120 , ASN R:180 , ASN R:313 , TYR R:317
BINDING SITE FOR RESIDUE NAD R 408
27
CC9
SOFTWARE
GLN Q:134 , ASP Q:135 , LYS Q:159
BINDING SITE FOR RESIDUE EDO Q 405
28
DC1
SOFTWARE
ARG Q:169 , LYS R:303
BINDING SITE FOR RESIDUE GOL R 409
29
DC2
SOFTWARE
GLY P:131 , GLN P:134 , ASP P:135 , LYS P:159
BINDING SITE FOR RESIDUE GOL P 404
30
DC3
SOFTWARE
ASP P:181 , ARG P:183 , PRO P:188 , HIS P:190 , LYS P:191
BINDING SITE FOR RESIDUE GOL P 405
31
DC4
SOFTWARE
LYS O:303 , ARG P:169
BINDING SITE FOR RESIDUE GOL O 408
32
DC5
SOFTWARE
GLN R:134 , ASP R:135
BINDING SITE FOR RESIDUE GOL R 410
33
DC6
SOFTWARE
LYS P:212 , ALA P:215 , GLY P:223
BINDING SITE FOR RESIDUE GOL P 406
34
DC7
SOFTWARE
ASN Q:14 , ARG Q:17 , HIS Q:50 , THR Q:315
BINDING SITE FOR RESIDUE GOL Q 406
35
DC8
SOFTWARE
HIS P:50 , GLY P:51 , ARG R:281
BINDING SITE FOR RESIDUE GOL P 407
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (O:147-154,P:147-154,Q:147-154,R: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.
G3P_GEOSE
150-157
4
O:147-154
P:147-154
Q:147-154
R:147-154
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3cmco2 (O:149-312)
1b: SCOP_d3cmcp2 (P:149-312)
1c: SCOP_d3cmcq2 (Q:149-312)
1d: SCOP_d3cmcr2 (R:149-312)
2a: SCOP_d3cmco1 (O:0-148,O:313-333)
2b: SCOP_d3cmcp1 (P:0-148,P:313-333)
2c: SCOP_d3cmcq1 (Q:0-148,Q:313-333)
2d: SCOP_d3cmcr1 (R:0-148,R:313-333)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
GAPDH-like
(99)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Bacillus stearothermophilus, nca 1503 [TaxId: 1422]
(11)
1a
d3cmco2
O:149-312
1b
d3cmcp2
P:149-312
1c
d3cmcq2
Q:149-312
1d
d3cmcr2
R:149-312
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Bacillus stearothermophilus, nca 1503 [TaxId: 1422]
(11)
2a
d3cmco1
O:0-148,O:313-333
2b
d3cmcp1
P:0-148,P:313-333
2c
d3cmcq1
Q:0-148,Q:313-333
2d
d3cmcr1
R:0-148,R:313-333
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3cmcO02 (O:148-313)
1b: CATH_3cmcP02 (P:148-313)
1c: CATH_3cmcQ02 (Q:148-313)
1d: CATH_3cmcR02 (R:148-313)
2a: CATH_3cmcO01 (O:0-147,O:314-333)
2b: CATH_3cmcP01 (P:0-147,P:314-333)
2c: CATH_3cmcQ01 (Q:0-147,Q:314-333)
2d: CATH_3cmcR01 (R:0-147,R:314-333)
View:
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Classes
(
)
(
)
Architectures
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)
(
)
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)
Bacillus stearothermophilus.
(1)
1a
3cmcO02
O:148-313
1b
3cmcP02
P:148-313
1c
3cmcQ02
Q:148-313
1d
3cmcR02
R:148-313
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Bacillus stearothermophilus.
(1)
2a
3cmcO01
O:0-147,O:314-333
2b
3cmcP01
P:0-147,P:314-333
2c
3cmcQ01
Q:0-147,Q:314-333
2d
3cmcR01
R:0-147,R:314-333
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Asym.Unit (262 KB)
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