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1RM5
Biol. Unit 2
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Asym.Unit (177 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (230 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MUTANT S188A OF PHOTOSYNTHETIC GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE A4 ISOFORM, COMPLEXED WITH NADP
Authors
:
F. Sparla, S. Fermani, G. Falini, A. Ripamonti, P. Sabatino, P. Pupillo
Date
:
27 Nov 03 (Deposition) - 27 Jul 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,O
Biol. Unit 1: A,B (2x)
Biol. Unit 2: O (4x)
Keywords
:
Rossmann Fold, Gapdh-Nadp Complex, Oxidoreductase
(Keyword Search:
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Reference
:
F. Sparla, S. Fermani, G. Falini, M. Zaffagnini, A. Ripamonti, P. Sabatino, P. Pupillo, P. Trost
Coenzyme Site-Directed Mutants Of Photosynthetic A(4)-Gapdh Show Selectively Reduced Nadph-Dependent Catalysis, Similar To Regulatory Ab-Gapdh Inhibited By Oxidized Thioredoxin
J. Mol. Biol. V. 340 1025 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 16)
Info
All Hetero Components
1a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
1b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
1c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
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)
View:
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Label:
No.
Name
Count
Type
Full Name
1
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2
SO4
12
Ligand/Ion
SULFATE ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC8 (SOFTWARE)
4: BC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR O:179 , ASP O:181 , ARG O:195 , ARG O:231 , NDP O:7335 , HOH O:7367 , HOH O:7448
BINDING SITE FOR RESIDUE SO4 O 7338
2
AC2
SOFTWARE
SER O:148 , THR O:208 , GLY O:209 , ALA O:210 , HOH O:7408 , HOH O:7471 , HOH O:7535
BINDING SITE FOR RESIDUE SO4 O 7339
3
AC8
SOFTWARE
LYS A:72 , HOH A:1352 , PHE O:251 , ALA O:252 , VAL O:299 , HOH O:7370 , HOH O:7459
BINDING SITE FOR RESIDUE SO4 O 902
4
BC2
SOFTWARE
GLY O:9 , ARG O:10 , ILE O:11 , 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 , SO4 O:7338 , HOH O:7354 , HOH O:7356 , HOH O:7357 , HOH O:7358 , HOH O:7368 , HOH O:7450 , HOH O:7506 , HOH O:7546 , HOH O:7548
BINDING SITE FOR RESIDUE NDP O 7335
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (O:147-154)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3PA_SPIOL
216-223
4
-
-
O:147-154
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Exons
(0, 0)
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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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1rm5a2 (A:149-312)
1b: SCOP_d1rm5b2 (B:149-312)
1c: SCOP_d1rm5o2 (O:149-312)
2a: SCOP_d1rm5a1 (A:1-148,A:313-333)
2b: SCOP_d1rm5b1 (B:1-148,B:313-333)
2c: SCOP_d1rm5o1 (O:1-148,O:313-333)
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)
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)
Protein Domains
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)
(
)
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)
Spinach (Spinacia oleracea) [TaxId: 3562]
(8)
1a
d1rm5a2
A:149-312
1b
d1rm5b2
B:149-312
1c
d1rm5o2
O: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)
Spinach (Spinacia oleracea) [TaxId: 3562]
(8)
2a
d1rm5a1
A:1-148,A:313-333
2b
d1rm5b1
B:1-148,B:313-333
2c
d1rm5o1
O:1-148,O:313-333
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1rm5A02 (A:148-313)
1b: CATH_1rm5B02 (B:148-313)
1c: CATH_1rm5O02 (O:148-313)
2a: CATH_1rm5A01 (A:1-147,A:314-333)
2b: CATH_1rm5B01 (B:1-147,B:314-333)
2c: CATH_1rm5O01 (O:1-147,O:314-333)
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)
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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)
Spinach (Spinacia oleracea)
(8)
1a
1rm5A02
A:148-313
1b
1rm5B02
B:148-313
1c
1rm5O02
O:148-313
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Spinach (Spinacia oleracea)
(10)
2a
1rm5A01
A:1-147,A:314-333
2b
1rm5B01
B:1-147,B:314-333
2c
1rm5O01
O:1-147,O:314-333
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_1rm5O01 (O:154-311)
1b: PFAM_Gp_dh_C_1rm5O02 (O:154-311)
1c: PFAM_Gp_dh_C_1rm5O03 (O:154-311)
2a: PFAM_Gp_dh_N_1rm5O04 (O:1-149)
2b: PFAM_Gp_dh_N_1rm5O05 (O:1-149)
2c: PFAM_Gp_dh_N_1rm5O06 (O:1-149)
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Clans
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)
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)
Families
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)
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)
Organisms
(
)
(
)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Spinacia oleracea (Spinach)
(5)
1a
Gp_dh_C-1rm5O01
O:154-311
1b
Gp_dh_C-1rm5O02
O:154-311
1c
Gp_dh_C-1rm5O03
O:154-311
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Spinacia oleracea (Spinach)
(5)
2a
Gp_dh_N-1rm5O04
O:1-149
2b
Gp_dh_N-1rm5O05
O:1-149
2c
Gp_dh_N-1rm5O06
O:1-149
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Asym.Unit (177 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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