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1DSS
Asym. Unit
Info
Asym.Unit (118 KB)
Biol.Unit 1 (221 KB)
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(1)
Title
:
STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR
Authors
:
S. Song, Z. Lin
Date
:
04 Jun 97 (Deposition) - 09 Dec 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.88
Chains
:
Asym. Unit : G,R
Biol. Unit 1: G,R (2x)
Keywords
:
Active-Site Carboxymethylation, D-Glyceraldehyde-3-Phosphate- Dehydrogenase, 'The-Half-Of-Sites' Reaction, Molecular Symmetry
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Y. Song, Y. B. Xu, Z. J. Lin, C. L. Tsou
Structure Of Active Site Carboxymethylated D-Glyceraldehyde-3-Phosphate Dehydrogenase From Palinurus Versicolor.
J. Mol. Biol. V. 287 719 1999
(for further references see the
PDB file header
)
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: CARBOXYMETHYLATED CYSTEINE (CCSa)
1b: CARBOXYMETHYLATED CYSTEINE (CCSb)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CCS
2
Mod. Amino Acid
CARBOXYMETHYLATED CYSTEINE
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AVG (UNKNOWN)
8: AVR (UNKNOWN)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER G:148 , CCS G:149 , THR G:150 , HIS G:176 , THR G:208 , GLY G:209 , HOH G:584 , HOH G:620 , HOH G:678 , HOH G:717
BINDING SITE FOR RESIDUE SO4 G 501
2
AC2
SOFTWARE
CCS G:149 , THR G:179 , THR G:181 , ARG G:231 , NAD G:335 , HOH G:530 , HOH G:717
BINDING SITE FOR RESIDUE SO4 G 502
3
AC3
SOFTWARE
SER R:148 , CCS R:149 , THR R:150 , HIS R:176 , THR R:208 , GLY R:209 , HOH R:611 , HOH R:675 , HOH R:676
BINDING SITE FOR RESIDUE SO4 R 501
4
AC4
SOFTWARE
CCS R:149 , THR R:179 , THR R:181 , ARG R:231 , NAD R:335 , HOH R:585 , HOH R:675
BINDING SITE FOR RESIDUE SO4 R 502
5
AC5
SOFTWARE
ASN G:6 , GLY G:7 , PHE G:8 , GLY G:9 , ARG G:10 , ILE G:11 , ASN G:31 , ASP G:32 , PRO G:33 , PHE G:34 , MET G:77 , SER G:95 , THR G:96 , GLY G:97 , SER G:119 , ALA G:120 , CCS G:149 , ALA G:180 , ASN G:313 , GLU G:314 , TYR G:317 , SO4 G:502 , HOH G:505 , HOH G:506 , HOH G:512 , HOH G:513 , HOH G:530 , HOH G:535 , HOH G:536 , HOH G:544 , HOH G:552 , HOH G:598 , HOH G:619 , HOH G:622 , HOH G:651
BINDING SITE FOR RESIDUE NAD G 335
6
AC6
SOFTWARE
ASN R:6 , GLY R:7 , GLY R:9 , ARG R:10 , ILE R:11 , ASN R:31 , ASP R:32 , PRO R:33 , PHE R:34 , GLU R:76 , MET R:77 , SER R:95 , THR R:96 , GLY R:97 , PHE R:99 , SER R:119 , ALA R:120 , CCS R:149 , ALA R:180 , ASN R:313 , GLU R:314 , TYR R:317 , SO4 R:502 , HOH R:510 , HOH R:511 , HOH R:512 , HOH R:533 , HOH R:534 , HOH R:535 , HOH R:544 , HOH R:585 , HOH R:589 , HOH R:590 , HOH R:591 , HOH R:615 , HOH R:656
BINDING SITE FOR RESIDUE NAD R 335
7
AVG
UNKNOWN
CCS G:149 , HIS G:176
ACTIVE SITE.
8
AVR
UNKNOWN
CCS R:149 , HIS R:176
ACTIVE SITE.
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: GAPDH (G:147-154,R:147-154)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3P_PANVR
146-153
2
G:147-154
R:147-154
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1dssg2 (G:149-312)
1b: SCOP_d1dssr2 (R:149-312)
2a: SCOP_d1dssg1 (G:1-148,G:313-334)
2b: SCOP_d1dssr1 (R:1-148,R:313-334)
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Superfamilies
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)
(
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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)
South China Sea lobster (Palinurus versicolor) [TaxId: 150436]
(5)
1a
d1dssg2
G:149-312
1b
d1dssr2
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)
South China Sea lobster (Palinurus versicolor) [TaxId: 150436]
(5)
2a
d1dssg1
G:1-148,G:313-334
2b
d1dssr1
R:1-148,R:313-334
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1dssG02 (G:148-313)
1b: CATH_1dssR02 (R:148-313)
2a: CATH_1dssG01 (G:1-147,G:314-333)
2b: CATH_1dssR01 (R:1-147,R:314-333)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
South china sea lobster (Palinurus versicolor)
(5)
1a
1dssG02
G:148-313
1b
1dssR02
R:148-313
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
South china sea lobster (Palinurus versicolor)
(5)
2a
1dssG01
G:1-147,G:314-333
2b
1dssR01
R:1-147,R:314-333
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain R
Asymmetric Unit 1
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Asym.Unit (118 KB)
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