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2PKR
Biol. Unit 3
Info
Asym.Unit (640 KB)
Biol.Unit 1 (217 KB)
Biol.Unit 2 (216 KB)
Biol.Unit 3 (215 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF (A+CTE)4 CHIMERIC FORM OF PHOTOSYNTETIC GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, COMPLEXED WITH NADP
Authors
:
S. Fermani, G. Falini, A. Ripamonti
Date
:
18 Apr 07 (Deposition) - 19 Jun 07 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,H,I,L,M,O,P,Q,R
Biol. Unit 1: O,P,Q,R (1x)
Biol. Unit 2: A,B,C,D (1x)
Biol. Unit 3: H,I,L,M (1x)
Keywords
:
Chimeric Protein, Rossmann Fold, Nadp Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Fermani, F. Sparla, G. Falini, P. L. Martelli, R. Casadio, P. Pupillo, A. Ripamonti, P. Trost
Molecular Mechanism Of Thioredoxin Regulation In Photosynthetic A2B2-Glyceraldehyde-3-Phosphate Dehydrogenase.
Proc. Natl. Acad. Sci. Usa V. 104 11109 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 15)
Info
All Hetero Components
1a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
1b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
1c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
1d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
1e: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPe)
1f: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPf)
1g: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPg)
1h: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPh)
1i: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPi)
1j: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPj)
1k: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPk)
1l: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPl)
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)
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
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2
SO4
11
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(15, 15)
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: EC7 (SOFTWARE)
13: EC8 (SOFTWARE)
14: EC9 (SOFTWARE)
15: FC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC6
SOFTWARE
THR H:179 , ASP H:181 , ARG H:195 , ARG H:231 , NDP H:379
BINDING SITE FOR RESIDUE SO4 H 363
02
CC7
SOFTWARE
SER H:148 , CYS H:149 , THR H:150 , HIS H:176 , THR H:208
BINDING SITE FOR RESIDUE SO4 H 364
03
CC8
SOFTWARE
PHE H:251 , ALA H:252 , GLU H:253 , VAL H:299
BINDING SITE FOR RESIDUE SO4 H 378
04
CC9
SOFTWARE
THR I:179 , ASP I:181 , ARG I:195 , ARG I:231 , NDP I:380
BINDING SITE FOR RESIDUE SO4 I 365
05
DC1
SOFTWARE
SER I:148 , THR I:208 , GLY I:209 , ALA I:210
BINDING SITE FOR RESIDUE SO4 I 366
06
DC2
SOFTWARE
GLU I:253 , ASN I:256 , ARG I:260 , SER I:294
BINDING SITE FOR RESIDUE SO4 I 379
07
DC3
SOFTWARE
THR L:179 , ASP L:181 , ARG L:195 , ARG L:231 , NDP L:369
BINDING SITE FOR RESIDUE SO4 L 367
08
DC4
SOFTWARE
SER L:148 , THR L:150 , HIS L:176 , THR L:208 , GLY L:209
BINDING SITE FOR RESIDUE SO4 L 368
09
DC5
SOFTWARE
THR M:179 , ASP M:181 , ARG M:195 , ARG M:231 , NDP M:381
BINDING SITE FOR RESIDUE SO4 M 369
10
DC6
SOFTWARE
SER M:148 , CYS M:149 , THR M:150 , THR M:208
BINDING SITE FOR RESIDUE SO4 M 370
11
DC7
SOFTWARE
SER M:62 , LYS M:72
BINDING SITE FOR RESIDUE SO4 M 380
12
EC7
SOFTWARE
PHE H:8 , GLY H:9 , ARG H:10 , ILE H:11 , ASN H:31 , ASP H:76 , ARG H:77 , GLY H:95 , THR H:96 , GLY H:97 , VAL H:98 , PHE H:99 , THR H:119 , ALA H:120 , CYS H:149 , ASN H:313 , TYR H:317 , SO4 H:363 , SER I:188
BINDING SITE FOR RESIDUE NDP H 379
13
EC8
SOFTWARE
ARG H:183 , SER H:188 , GLY I:7 , PHE I:8 , GLY I:9 , ARG I:10 , ILE I:11 , ASN I:31 , ASP I:76 , ARG I:77 , GLY I:95 , THR I:96 , GLY I:97 , VAL I:98 , PHE I:99 , THR I:119 , ALA I:120 , ASN I:313 , TYR I:317 , SO4 I:365
BINDING SITE FOR RESIDUE NDP I 380
14
EC9
SOFTWARE
GLY L:7 , PHE L:8 , GLY L:9 , ARG L:10 , ILE L:11 , ASN L:31 , ASP L:76 , ARG L:77 , GLY L:95 , THR L:96 , GLY L:97 , VAL L:98 , PHE L:99 , THR L:119 , ALA L:120 , CYS L:149 , ASN L:313 , TYR L:317 , SO4 L:367 , ARG M:183 , SER M:188
BINDING SITE FOR RESIDUE NDP L 369
15
FC1
SOFTWARE
SER L:188 , GLY M:7 , PHE M:8 , GLY M:9 , ARG M:10 , ILE M:11 , ASN M:31 , ASP M:76 , ARG M:77 , GLY M:95 , THR M:96 , GLY M:97 , VAL M:98 , PHE M:99 , THR M:119 , ALA M:120 , ASN M:313 , TYR M:317 , SO4 M:369
BINDING SITE FOR RESIDUE NDP M 381
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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 (H:147-154,I:147-154,L:147-154,M: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.
G3PA_SPIOL
216-223
4
-
-
-
-
H:147-154
I:147-154
L:147-154
M:147-154
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(2, 24)
Info
All SCOP Domains
1a: SCOP_d2pkra2 (A:149-312)
1b: SCOP_d2pkrb2 (B:149-312)
1c: SCOP_d2pkrc2 (C:149-312)
1d: SCOP_d2pkrd2 (D:149-312)
1e: SCOP_d2pkrh2 (H:149-312)
1f: SCOP_d2pkri2 (I:149-312)
1g: SCOP_d2pkrl2 (L:149-312)
1h: SCOP_d2pkrm2 (M:149-312)
1i: SCOP_d2pkro2 (O:149-312)
1j: SCOP_d2pkrp2 (P:149-312)
1k: SCOP_d2pkrq2 (Q:149-312)
1l: SCOP_d2pkrr2 (R:149-312)
2a: SCOP_d2pkra1 (A:0-148,A:313-333)
2b: SCOP_d2pkrb1 (B:0-148,B:313-333)
2c: SCOP_d2pkrc1 (C:0-148,C:313-333)
2d: SCOP_d2pkrd1 (D:0-148,D:313-333)
2e: SCOP_d2pkrh1 (H:0-148,H:313-333)
2f: SCOP_d2pkri1 (I:0-148,I:313-333)
2g: SCOP_d2pkrl1 (L:0-148,L:313-333)
2h: SCOP_d2pkrm1 (M:0-148,M:313-333)
2i: SCOP_d2pkro1 (O:0-148,O:313-333)
2j: SCOP_d2pkrp1 (P:0-148,P:313-333)
2k: SCOP_d2pkrq1 (Q:0-148,Q:313-333)
2l: SCOP_d2pkrr1 (R:0-148,R:313-333)
View:
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Label:
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)
Spinach (Spinacia oleracea) [TaxId: 3562]
(8)
1a
d2pkra2
A:149-312
1b
d2pkrb2
B:149-312
1c
d2pkrc2
C:149-312
1d
d2pkrd2
D:149-312
1e
d2pkrh2
H:149-312
1f
d2pkri2
I:149-312
1g
d2pkrl2
L:149-312
1h
d2pkrm2
M:149-312
1i
d2pkro2
O:149-312
1j
d2pkrp2
P:149-312
1k
d2pkrq2
Q:149-312
1l
d2pkrr2
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)
Spinach (Spinacia oleracea) [TaxId: 3562]
(8)
2a
d2pkra1
A:0-148,A:313-333
2b
d2pkrb1
B:0-148,B:313-333
2c
d2pkrc1
C:0-148,C:313-333
2d
d2pkrd1
D:0-148,D:313-333
2e
d2pkrh1
H:0-148,H:313-333
2f
d2pkri1
I:0-148,I:313-333
2g
d2pkrl1
L:0-148,L:313-333
2h
d2pkrm1
M:0-148,M:313-333
2i
d2pkro1
O:0-148,O:313-333
2j
d2pkrp1
P:0-148,P:313-333
2k
d2pkrq1
Q:0-148,Q:313-333
2l
d2pkrr1
R:0-148,R:313-333
[
close SCOP info
]
CATH Domains
(2, 24)
Info
all CATH domains
1a: CATH_2pkrA02 (A:148-313)
1b: CATH_2pkrH02 (H:148-313)
1c: CATH_2pkrI02 (I:148-313)
1d: CATH_2pkrL02 (L:148-313)
1e: CATH_2pkrM02 (M:148-313)
1f: CATH_2pkrO02 (O:148-313)
1g: CATH_2pkrP02 (P:148-313)
1h: CATH_2pkrQ02 (Q:148-313)
1i: CATH_2pkrR02 (R:148-313)
1j: CATH_2pkrB02 (B:148-313)
1k: CATH_2pkrC02 (C:148-313)
1l: CATH_2pkrD02 (D:148-313)
2a: CATH_2pkrA01 (A:1-147,A:314-333)
2b: CATH_2pkrB01 (B:1-147,B:314-333)
2c: CATH_2pkrC01 (C:1-147,C:314-333)
2d: CATH_2pkrD01 (D:1-147,D:314-333)
2e: CATH_2pkrH01 (H:1-147,H:314-333)
2f: CATH_2pkrI01 (I:1-147,I:314-333)
2g: CATH_2pkrL01 (L:1-147,L:314-333)
2h: CATH_2pkrM01 (M:1-147,M:314-333)
2i: CATH_2pkrO01 (O:1-147,O:314-333)
2j: CATH_2pkrP01 (P:1-147,P:314-333)
2k: CATH_2pkrQ01 (Q:1-147,Q:314-333)
2l: CATH_2pkrR01 (R:1-147,R: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)
Spinach (Spinacia oleracea)
(8)
1a
2pkrA02
A:148-313
1b
2pkrH02
H:148-313
1c
2pkrI02
I:148-313
1d
2pkrL02
L:148-313
1e
2pkrM02
M:148-313
1f
2pkrO02
O:148-313
1g
2pkrP02
P:148-313
1h
2pkrQ02
Q:148-313
1i
2pkrR02
R:148-313
1j
2pkrB02
B:148-313
1k
2pkrC02
C:148-313
1l
2pkrD02
D: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
2pkrA01
A:1-147,A:314-333
2b
2pkrB01
B:1-147,B:314-333
2c
2pkrC01
C:1-147,C:314-333
2d
2pkrD01
D:1-147,D:314-333
2e
2pkrH01
H:1-147,H:314-333
2f
2pkrI01
I:1-147,I:314-333
2g
2pkrL01
L:1-147,L:314-333
2h
2pkrM01
M:1-147,M:314-333
2i
2pkrO01
O:1-147,O:314-333
2j
2pkrP01
P:1-147,P:314-333
2k
2pkrQ01
Q:1-147,Q:314-333
2l
2pkrR01
R:1-147,R:314-333
[
close CATH info
]
Pfam Domains
(2, 24)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_2pkrR01 (R:154-311)
1b: PFAM_Gp_dh_C_2pkrR02 (R:154-311)
1c: PFAM_Gp_dh_C_2pkrR03 (R:154-311)
1d: PFAM_Gp_dh_C_2pkrR04 (R:154-311)
1e: PFAM_Gp_dh_C_2pkrR05 (R:154-311)
1f: PFAM_Gp_dh_C_2pkrR06 (R:154-311)
1g: PFAM_Gp_dh_C_2pkrR07 (R:154-311)
1h: PFAM_Gp_dh_C_2pkrR08 (R:154-311)
1i: PFAM_Gp_dh_C_2pkrR09 (R:154-311)
1j: PFAM_Gp_dh_C_2pkrR10 (R:154-311)
1k: PFAM_Gp_dh_C_2pkrR11 (R:154-311)
1l: PFAM_Gp_dh_C_2pkrR12 (R:154-311)
2a: PFAM_Gp_dh_N_2pkrR13 (R:1-149)
2b: PFAM_Gp_dh_N_2pkrR14 (R:1-149)
2c: PFAM_Gp_dh_N_2pkrR15 (R:1-149)
2d: PFAM_Gp_dh_N_2pkrR16 (R:1-149)
2e: PFAM_Gp_dh_N_2pkrR17 (R:1-149)
2f: PFAM_Gp_dh_N_2pkrR18 (R:1-149)
2g: PFAM_Gp_dh_N_2pkrR19 (R:1-149)
2h: PFAM_Gp_dh_N_2pkrR20 (R:1-149)
2i: PFAM_Gp_dh_N_2pkrR21 (R:1-149)
2j: PFAM_Gp_dh_N_2pkrR22 (R:1-149)
2k: PFAM_Gp_dh_N_2pkrR23 (R:1-149)
2l: PFAM_Gp_dh_N_2pkrR24 (R:1-149)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Spinacia oleracea (Spinach)
(5)
1a
Gp_dh_C-2pkrR01
R:154-311
1b
Gp_dh_C-2pkrR02
R:154-311
1c
Gp_dh_C-2pkrR03
R:154-311
1d
Gp_dh_C-2pkrR04
R:154-311
1e
Gp_dh_C-2pkrR05
R:154-311
1f
Gp_dh_C-2pkrR06
R:154-311
1g
Gp_dh_C-2pkrR07
R:154-311
1h
Gp_dh_C-2pkrR08
R:154-311
1i
Gp_dh_C-2pkrR09
R:154-311
1j
Gp_dh_C-2pkrR10
R:154-311
1k
Gp_dh_C-2pkrR11
R:154-311
1l
Gp_dh_C-2pkrR12
R:154-311
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Spinacia oleracea (Spinach)
(5)
2a
Gp_dh_N-2pkrR13
R:1-149
2b
Gp_dh_N-2pkrR14
R:1-149
2c
Gp_dh_N-2pkrR15
R:1-149
2d
Gp_dh_N-2pkrR16
R:1-149
2e
Gp_dh_N-2pkrR17
R:1-149
2f
Gp_dh_N-2pkrR18
R:1-149
2g
Gp_dh_N-2pkrR19
R:1-149
2h
Gp_dh_N-2pkrR20
R:1-149
2i
Gp_dh_N-2pkrR21
R:1-149
2j
Gp_dh_N-2pkrR22
R:1-149
2k
Gp_dh_N-2pkrR23
R:1-149
2l
Gp_dh_N-2pkrR24
R:1-149
[
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]
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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