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1RM4
Asym. Unit
Info
Asym.Unit (178 KB)
Biol.Unit 1 (224 KB)
Biol.Unit 2 (234 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RECOMBINANT 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
:
2.00
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, 11)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NDP
3
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2
SO4
8
Ligand/Ion
SULFATE ION
[
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR O:179 , ASP O:181 , ARG O:195 , ARG O:231 , NDP O:7335 , HOH O:7357 , HOH O:7453 , HOH O:7460 , HOH O:7594
BINDING SITE FOR RESIDUE SO4 O 7338
02
AC2
SOFTWARE
SER O:148 , CYS O:149 , THR O:150 , THR O:208 , HOH O:7391
BINDING SITE FOR RESIDUE SO4 O 7339
03
AC3
SOFTWARE
THR A:179 , ASP A:181 , ARG A:195 , ARG A:231 , NDP A:1335 , HOH A:1395
BINDING SITE FOR RESIDUE SO4 A 1338
04
AC4
SOFTWARE
SER A:148 , THR A:208 , GLY A:209 , ALA A:210 , HOH A:1356 , HOH A:1396
BINDING SITE FOR RESIDUE SO4 A 1339
05
AC5
SOFTWARE
THR B:179 , ASP B:181 , ARG B:195 , ARG B:231 , NDP B:2335 , HOH B:2402
BINDING SITE FOR RESIDUE SO4 B 2338
06
AC6
SOFTWARE
SER B:148 , THR B:150 , THR B:208 , GLY B:209 , ALA B:210 , HOH B:2388
BINDING SITE FOR RESIDUE SO4 B 2339
07
AC7
SOFTWARE
GLY A:36 , VAL A:37 , LYS A:38 , HOH A:1341
BINDING SITE FOR RESIDUE SO4 A 901
08
AC8
SOFTWARE
LEU A:201 , ARG A:284 , HOH A:1459 , HOH A:1464 , ARG B:284 , HOH B:2366
BINDING SITE FOR RESIDUE SO4 B 902
09
AC9
SOFTWARE
GLY O:7 , PHE O:8 , GLY O:9 , ARG O:10 , ILE O:11 , ASN O:31 , ASP O:76 , ARG O:77 , GLY O:95 , THR O:96 , GLY O:97 , PHE O:99 , THR O:119 , ALA O:120 , ARG O:183 , SER O:188 , ASN O:313 , GLU O:314 , TYR O:317 , SO4 O:7338 , HOH O:7348 , HOH O:7367 , HOH O:7372 , HOH O:7424 , HOH O:7430 , HOH O:7532 , HOH O:7533 , HOH O:7535 , HOH O:7570
BINDING SITE FOR RESIDUE NDP O 7335
10
BC1
SOFTWARE
GLY A:7 , ARG A:10 , ILE A:11 , ASN A:31 , THR A:33 , ARG A:77 , GLY A:95 , THR A:96 , GLY A:97 , PHE A:99 , THR A:119 , ALA A:120 , ASN A:313 , TYR A:317 , SO4 A:1338 , HOH A:1343 , HOH A:1346 , HOH A:1348 , HOH A:1353 , HOH A:1358 , HOH A:1395 , HOH A:1417 , HOH A:1425 , HOH A:1457 , HOH A:1479 , HOH A:1480 , SER B:188
BINDING SITE FOR RESIDUE NDP A 1335
11
BC2
SOFTWARE
SER A:188 , GLY B:7 , GLY B:9 , ARG B:10 , ILE B:11 , ARG B:77 , GLY B:95 , THR B:96 , GLY B:97 , THR B:119 , ALA B:120 , ASN B:313 , GLU B:314 , TYR B:317 , SO4 B:2338 , HOH B:2359 , HOH B:2368 , HOH B:2402 , HOH B:2404 , HOH B:2442
BINDING SITE FOR RESIDUE NDP B 2335
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: GAPDH (A:147-154,B:147-154,O:147-154)
;
View:
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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
3
A:147-154
B:147-154
O:147-154
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Exons
(0, 0)
Info
All Exons
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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, 6)
Info
All SCOP Domains
1a: SCOP_d1rm4a2 (A:149-312)
1b: SCOP_d1rm4b2 (B:149-312)
1c: SCOP_d1rm4o2 (O:149-312)
2a: SCOP_d1rm4a1 (A:1-148,A:313-333)
2b: SCOP_d1rm4b1 (B:1-148,B:313-333)
2c: SCOP_d1rm4o1 (O:1-148,O:313-333)
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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
d1rm4a2
A:149-312
1b
d1rm4b2
B:149-312
1c
d1rm4o2
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
d1rm4a1
A:1-148,A:313-333
2b
d1rm4b1
B:1-148,B:313-333
2c
d1rm4o1
O:1-148,O:313-333
[
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]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1rm4A02 (A:148-313)
1b: CATH_1rm4B02 (B:148-313)
1c: CATH_1rm4O02 (O:148-313)
2a: CATH_1rm4A01 (A:1-147,A:314-333)
2b: CATH_1rm4O01 (O:1-147,O:314-333)
2c: CATH_1rm4B01 (B:1-147,B: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)
Spinach (Spinacia oleracea)
(8)
1a
1rm4A02
A:148-313
1b
1rm4B02
B:148-313
1c
1rm4O02
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
1rm4A01
A:1-147,A:314-333
2b
1rm4O01
O:1-147,O:314-333
2c
1rm4B01
B:1-147,B:314-333
[
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_1rm4O01 (O:154-311)
1b: PFAM_Gp_dh_C_1rm4O02 (O:154-311)
1c: PFAM_Gp_dh_C_1rm4O03 (O:154-311)
2a: PFAM_Gp_dh_N_1rm4O04 (O:1-149)
2b: PFAM_Gp_dh_N_1rm4O05 (O:1-149)
2c: PFAM_Gp_dh_N_1rm4O06 (O:1-149)
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Clans
(
)
(
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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-1rm4O01
O:154-311
1b
Gp_dh_C-1rm4O02
O:154-311
1c
Gp_dh_C-1rm4O03
O:154-311
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Spinacia oleracea (Spinach)
(5)
2a
Gp_dh_N-1rm4O04
O:1-149
2b
Gp_dh_N-1rm4O05
O:1-149
2c
Gp_dh_N-1rm4O06
O:1-149
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