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3K2B
Biol. Unit 2
Info
Asym.Unit (556 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (221 KB)
Biol.Unit 3 (228 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PHOTOSYNTHETIC A4 ISOFORM GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE COMPLEXED WITH NAD, FROM ARABIDOPSIS THALIANA
Authors
:
S. Fermani, G. Falini, A. Thumiger, F. Sparla, L. Marri, P. Trost
Date
:
29 Sep 09 (Deposition) - 09 Jun 10 (Release) - 02 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,O,Q
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: O,Q (2x)
Keywords
:
Rossmann Fold, Calvin Cycle, Chloroplast, Membrane, Nadp, Oxidoreductase, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Fermani, F. Sparla, L. Marri, A. Thumiger, P. Pupillo, G. Falini, P. Trost
Structure Of Photosynthetic Glyceraldehyde-3-Phosphate Dehydrogenase (Isoform A4) From Arabidopsis Thaliana In Complex With Nad
Acta Crystallogr. , Sect. F V. 66 621 2010
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 19)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
1e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
1g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
1h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
1i: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADi)
1j: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADj)
2a: SULFATE ION (SO4a)
2aa: SULFATE ION (SO4aa)
2ab: SULFATE ION (SO4ab)
2ac: SULFATE ION (SO4ac)
2ad: SULFATE ION (SO4ad)
2ae: SULFATE ION (SO4ae)
2af: SULFATE ION (SO4af)
2ag: SULFATE ION (SO4ag)
2ah: SULFATE ION (SO4ah)
2ai: SULFATE ION (SO4ai)
2aj: SULFATE ION (SO4aj)
2ak: SULFATE ION (SO4ak)
2al: SULFATE ION (SO4al)
2am: SULFATE ION (SO4am)
2an: SULFATE ION (SO4an)
2ao: SULFATE ION (SO4ao)
2ap: SULFATE ION (SO4ap)
2aq: SULFATE ION (SO4aq)
2ar: SULFATE ION (SO4ar)
2as: SULFATE ION (SO4as)
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)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
2x: SULFATE ION (SO4x)
2y: SULFATE ION (SO4y)
2z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
SO4
15
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(19, 19)
Info
All Sites
01: CC6 (SOFTWARE)
02: CC7 (SOFTWARE)
03: CC8 (SOFTWARE)
04: CC9 (SOFTWARE)
05: DC1 (SOFTWARE)
06: DC2 (SOFTWARE)
07: DC3 (SOFTWARE)
08: DC4 (SOFTWARE)
09: DC5 (SOFTWARE)
10: DC6 (SOFTWARE)
11: DC7 (SOFTWARE)
12: DC8 (SOFTWARE)
13: DC9 (SOFTWARE)
14: EC1 (SOFTWARE)
15: EC2 (SOFTWARE)
16: EC3 (SOFTWARE)
17: EC4 (SOFTWARE)
18: EC5 (SOFTWARE)
19: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC6
SOFTWARE
GLY E:7 , PHE E:8 , GLY E:9 , ARG E:10 , ILE E:11 , ASN E:31 , THR E:33 , ARG E:77 , GLY E:95 , THR E:96 , GLY E:97 , THR E:119 , ALA E:120 , CYS E:149 , THR E:179 , ASN E:313 , GLU E:314 , TYR E:317 , SO4 E:336
BINDING SITE FOR RESIDUE NAD E 335
02
CC7
SOFTWARE
THR E:179 , ASP E:181 , ARG E:195 , ARG E:231 , NAD E:335
BINDING SITE FOR RESIDUE SO4 E 336
03
CC8
SOFTWARE
SER E:148 , THR E:150 , THR E:208 , GLY E:209 , ALA E:210
BINDING SITE FOR RESIDUE SO4 E 337
04
CC9
SOFTWARE
GLU E:253 , ASN E:256 , ARG E:260 , SER E:294 , HOH E:536
BINDING SITE FOR RESIDUE SO4 E 334
05
DC1
SOFTWARE
ASP E:135 , ILE E:327 , ASN E:331
BINDING SITE FOR RESIDUE SO4 E 338
06
DC2
SOFTWARE
GLY F:7 , GLY F:9 , ARG F:10 , ILE F:11 , ASP F:32 , ARG F:77 , GLY F:95 , THR F:96 , GLY F:97 , VAL F:98 , PHE F:99 , THR F:119 , ALA F:120 , CYS F:149 , ASN F:313 , TYR F:317 , SER G:188
BINDING SITE FOR RESIDUE NAD F 335
07
DC3
SOFTWARE
THR F:179 , ASP F:181 , ARG F:195 , ARG F:231
BINDING SITE FOR RESIDUE SO4 F 336
08
DC4
SOFTWARE
SER F:148 , THR F:150 , THR F:208 , GLY F:209 , ALA F:210
BINDING SITE FOR RESIDUE SO4 F 337
09
DC5
SOFTWARE
GLU F:253 , ASN F:256 , ARG F:260 , ASP F:275
BINDING SITE FOR RESIDUE SO4 F 334
10
DC6
SOFTWARE
GLY G:7 , GLY G:9 , ARG G:10 , ILE G:11 , ASP G:32 , THR G:33 , ARG G:77 , THR G:96 , GLY G:97 , PHE G:99 , THR G:119 , ALA G:120 , CYS G:149 , THR G:179 , ASN G:313 , GLU G:314 , TYR G:317 , SO4 G:336 , HOH G:340
BINDING SITE FOR RESIDUE NAD G 335
11
DC7
SOFTWARE
THR G:179 , ASP G:181 , ARG G:195 , ARG G:231 , NAD G:335
BINDING SITE FOR RESIDUE SO4 G 336
12
DC8
SOFTWARE
SER G:148 , THR G:150 , THR G:208 , GLY G:209 , ALA G:210
BINDING SITE FOR RESIDUE SO4 G 337
13
DC9
SOFTWARE
THR G:127 , LEU G:216
BINDING SITE FOR RESIDUE SO4 G 334
14
EC1
SOFTWARE
SER G:138 , HIS G:139 , ASP G:140
BINDING SITE FOR RESIDUE SO4 G 338
15
EC2
SOFTWARE
GLU G:253 , ASN G:256 , ARG G:260 , HOH G:344 , HOH G:652
BINDING SITE FOR RESIDUE SO4 G 339
16
EC3
SOFTWARE
SER E:188 , GLY H:7 , PHE H:8 , GLY H:9 , ARG H:10 , ILE H:11 , ASP H:32 , THR H:33 , ARG H:77 , GLY H:95 , THR H:96 , GLY H:97 , VAL H:98 , THR H:119 , ALA H:120 , CYS H:149 , THR H:179 , ASN H:313 , GLU H:314 , TYR H:317 , SO4 H:336
BINDING SITE FOR RESIDUE NAD H 335
17
EC4
SOFTWARE
THR H:179 , ASP H:181 , ARG H:195 , ARG H:231 , NAD H:335
BINDING SITE FOR RESIDUE SO4 H 336
18
EC5
SOFTWARE
SER H:148 , THR H:150 , SER H:207 , THR H:208 , ALA H:210 , HOH H:861 , HOH H:862
BINDING SITE FOR RESIDUE SO4 H 337
19
EC6
SOFTWARE
GLU H:253 , ASN H:256 , ARG H:260 , SER H:294
BINDING SITE FOR RESIDUE SO4 H 334
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (E:147-154,F:147-154,G:147-154,H: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.
G3PA1_ARATH
211-218
4
-
-
-
-
E:147-154
F:147-154
G:147-154
H:147-154
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
[
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CATH Domains
(2, 20)
Info
all CATH domains
1a: CATH_3k2bA02 (A:148-313)
1b: CATH_3k2bC02 (C:148-313)
1c: CATH_3k2bD02 (D:148-313)
1d: CATH_3k2bE02 (E:148-313)
1e: CATH_3k2bF02 (F:148-313)
1f: CATH_3k2bG02 (G:148-313)
1g: CATH_3k2bH02 (H:148-313)
1h: CATH_3k2bO02 (O:148-313)
1i: CATH_3k2bQ02 (Q:148-313)
1j: CATH_3k2bB02 (B:148-313)
2a: CATH_3k2bA01 (A:1-147,A:314-333)
2b: CATH_3k2bO01 (O:1-147,O:314-333)
2c: CATH_3k2bQ01 (Q:1-147,Q:314-333)
2d: CATH_3k2bE01 (E:1-147,E:314-332)
2e: CATH_3k2bH01 (H:1-147,H:314-332)
2f: CATH_3k2bB01 (B:1-147,B:314-333)
2g: CATH_3k2bC01 (C:1-147,C:314-333)
2h: CATH_3k2bD01 (D:1-147,D:314-333)
2i: CATH_3k2bF01 (F:1-147,F:314-333)
2j: CATH_3k2bG01 (G:1-147,G:314-333)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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)
Thale cress (Arabidopsis thaliana)
(3)
1a
3k2bA02
A:148-313
1b
3k2bC02
C:148-313
1c
3k2bD02
D:148-313
1d
3k2bE02
E:148-313
1e
3k2bF02
F:148-313
1f
3k2bG02
G:148-313
1g
3k2bH02
H:148-313
1h
3k2bO02
O:148-313
1i
3k2bQ02
Q:148-313
1j
3k2bB02
B:148-313
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Thale cress (Arabidopsis thaliana)
(15)
2a
3k2bA01
A:1-147,A:314-333
2b
3k2bO01
O:1-147,O:314-333
2c
3k2bQ01
Q:1-147,Q:314-333
2d
3k2bE01
E:1-147,E:314-332
2e
3k2bH01
H:1-147,H:314-332
2f
3k2bB01
B:1-147,B:314-333
2g
3k2bC01
C:1-147,C:314-333
2h
3k2bD01
D:1-147,D:314-333
2i
3k2bF01
F:1-147,F:314-333
2j
3k2bG01
G:1-147,G:314-333
[
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]
Pfam Domains
(0, 0)
Info
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