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1ML3
Asym. Unit
Info
Asym.Unit (246 KB)
Biol.Unit 1 (239 KB)
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(1)
Title
:
EVIDENCES FOR A FLIP-FLOP CATALYTIC MECHANISM OF TRYPANOSOMA CRUZI GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, FROM ITS CRYSTAL STRUCTURE IN COMPLEX WITH REACTED IRREVERSIBLE INHIBITOR 2-(2-PHOSPHONO-ETHYL)-ACRYLIC ACID 4-NITRO-PHENYL ESTER
Authors
:
M. S. Castilho, F. Pavao, G. Oliva
Date
:
29 Aug 02 (Deposition) - 08 Jul 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Protein Covalent-Inhibitor Complex, Oxidoreductase
(Keyword Search:
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Reference
:
M. S. Castilho, F. Pavao, G. Oliva, S. Ladame, M. Willson, J. Perie
Evidence For The Two Phosphate Binding Sites Of An Analogue Of The Thioacyl Intermediate For The Trypanosoma Cruzi Glyceraldehyde-3-Phosphate Dehydrogenase-Catalyzed Reaction, From Its Crystal Structure.
Biochemistry V. 42 7143 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: (3-FORMYL-BUT-3-ENYL)-PHOSPHONIC A... (CYXa)
1b: (3-FORMYL-BUT-3-ENYL)-PHOSPHONIC A... (CYXb)
1c: (3-FORMYL-BUT-3-ENYL)-PHOSPHONIC A... (CYXc)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CYX
3
Ligand/Ion
(3-FORMYL-BUT-3-ENYL)-PHOSPHONIC ACID
2
NAD
3
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL B:206 , GLY C:9 , GLY C:11 , ARG C:12 , ILE C:13 , ASP C:38 , MET C:39 , ALA C:90 , GLN C:91 , SER C:110 , THR C:111 , GLY C:112 , SER C:134 , ALA C:135 , CYS C:166 , ALA C:198 , ASN C:335 , TYR C:339 , CYX C:2166 , HOH C:2211 , HOH C:2222 , HOH C:2230 , HOH C:2274
BINDING SITE FOR RESIDUE NAD C 1360
2
AC2
SOFTWARE
ASN D:8 , GLY D:9 , GLY D:11 , ARG D:12 , ILE D:13 , VAL D:37 , ASP D:38 , MET D:39 , ALA D:90 , GLN D:91 , SER D:110 , THR D:111 , GLY D:112 , LEU D:113 , SER D:134 , ALA D:135 , ALA D:198 , ASN D:335 , TYR D:339 , CYX D:3166 , HOH D:3168 , HOH D:3174 , HOH D:3191 , HOH D:3192 , HOH D:3216 , HOH D:3301
BINDING SITE FOR RESIDUE NAD D 1361
3
AC3
SOFTWARE
GLY B:9 , GLY B:11 , ARG B:12 , ILE B:13 , ASP B:38 , MET B:39 , ALA B:90 , ARG B:92 , LEU B:113 , ALA B:135 , CYS B:166 , ALA B:198 , ASN B:335 , TYR B:339 , CYX B:1166 , HOH B:1450 , HOH B:1465 , HOH B:1516 , VAL C:206
BINDING SITE FOR RESIDUE NAD B 1362
4
AC4
SOFTWARE
CYS B:166 , THR B:167 , HIS B:194 , THR B:197 , THR B:226 , SER B:247 , ARG B:249 , NAD B:1362
BINDING SITE FOR RESIDUE CYX B 1166
5
AC5
SOFTWARE
SER C:165 , CYS C:166 , THR C:167 , HIS C:194 , THR C:197 , THR C:199 , THR C:225 , THR C:226 , SER C:247 , ARG C:249 , ASN C:335 , NAD C:1360 , HOH C:2274
BINDING SITE FOR RESIDUE CYX C 2166
6
AC6
SOFTWARE
CYS D:166 , HIS D:194 , THR D:197 , THR D:199 , ARG D:249 , ASN D:335 , NAD D:1361
BINDING SITE FOR RESIDUE CYX D 3166
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (A:164-171,B:164-171,C:164-171,D:16...)
;
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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.
G3PG_TRYCR
164-171
4
A:164-171
B:164-171
C:164-171
D:164-171
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Exons
(0, 0)
Info
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1ml3a2 (A:165-333)
1b: SCOP_d1ml3b2 (B:165-333)
1c: SCOP_d1ml3c2 (C:165-333)
1d: SCOP_d1ml3d2 (D:165-333)
2a: SCOP_d1ml3a1 (A:1-164,A:334-359)
2b: SCOP_d1ml3b1 (B:1-164,B:334-359)
2c: SCOP_d1ml3c1 (C:1-164,C:334-359)
2d: SCOP_d1ml3d1 (D:1-164,D:334-359)
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)
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)
(
)
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)
Trypanosoma cruzi [TaxId: 5693]
(5)
1a
d1ml3a2
A:165-333
1b
d1ml3b2
B:165-333
1c
d1ml3c2
C:165-333
1d
d1ml3d2
D:165-333
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)
Trypanosoma cruzi [TaxId: 5693]
(5)
2a
d1ml3a1
A:1-164,A:334-359
2b
d1ml3b1
B:1-164,B:334-359
2c
d1ml3c1
C:1-164,C:334-359
2d
d1ml3d1
D:1-164,D:334-359
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ml3A02 (A:165-335)
1b: CATH_1ml3B02 (B:165-335)
1c: CATH_1ml3C02 (C:165-335)
1d: CATH_1ml3D02 (D:165-335)
2a: CATH_1ml3A01 (A:2-164,A:336-355)
2b: CATH_1ml3B01 (B:2-164,B:336-355)
2c: CATH_1ml3C01 (C:2-164,C:336-355)
2d: CATH_1ml3D01 (D:2-164,D:336-355)
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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)
Trypanosoma cruzi. Organism_taxid: 5693.
(2)
1a
1ml3A02
A:165-335
1b
1ml3B02
B:165-335
1c
1ml3C02
C:165-335
1d
1ml3D02
D:165-335
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Trypanosoma cruzi. Organism_taxid: 5693.
(2)
2a
1ml3A01
A:2-164,A:336-355
2b
1ml3B01
B:2-164,B:336-355
2c
1ml3C01
C:2-164,C:336-355
2d
1ml3D01
D:2-164,D:336-355
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_1ml3D01 (D:171-333)
1b: PFAM_Gp_dh_C_1ml3D02 (D:171-333)
1c: PFAM_Gp_dh_C_1ml3D03 (D:171-333)
1d: PFAM_Gp_dh_C_1ml3D04 (D:171-333)
2a: PFAM_Gp_dh_N_1ml3D05 (D:3-166)
2b: PFAM_Gp_dh_N_1ml3D06 (D:3-166)
2c: PFAM_Gp_dh_N_1ml3D07 (D:3-166)
2d: PFAM_Gp_dh_N_1ml3D08 (D:3-166)
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Clans
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(
)
Organisms
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)
(
)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Trypanosoma cruzi
(2)
1a
Gp_dh_C-1ml3D01
D:171-333
1b
Gp_dh_C-1ml3D02
D:171-333
1c
Gp_dh_C-1ml3D03
D:171-333
1d
Gp_dh_C-1ml3D04
D:171-333
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Trypanosoma cruzi
(2)
2a
Gp_dh_N-1ml3D05
D:3-166
2b
Gp_dh_N-1ml3D06
D:3-166
2c
Gp_dh_N-1ml3D07
D:3-166
2d
Gp_dh_N-1ml3D08
D:3-166
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