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1DFO
Biol. Unit 2
Info
Asym.Unit (272 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (135 KB)
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(1)
Title
:
CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE
Authors
:
J. N. Scarsdale, S. Radaev, G. Kazanina, V. Schirch, H. T. Wright
Date
:
20 Nov 99 (Deposition) - 10 Dec 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Alpha Plp Aspartate, Amino Transferase, (Aat)-Like Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. N. Scarsdale, S. Radaev, G. Kazanina, V. Schirch, H. T. Wright
Crystal Structure At 2. 4 A Resolution Of E. Coli Serine Hydroxymethyltransferase In Complex With Glycine Substrate And 5-Formyl Tetrahydrofolate.
J. Mol. Biol. V. 296 155 2000
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 5-FORMYL-6-HYDROFOLIC ACID (FFOa)
1b: 5-FORMYL-6-HYDROFOLIC ACID (FFOb)
1c: 5-FORMYL-6-HYDROFOLIC ACID (FFOc)
1d: 5-FORMYL-6-HYDROFOLIC ACID (FFOd)
2a: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PH... (PLGa)
2b: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PH... (PLGb)
2c: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PH... (PLGc)
2d: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PH... (PLGd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
FFO
2
Ligand/Ion
5-FORMYL-6-HYDROFOLIC ACID
2
PLG
2
Ligand/Ion
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
[
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Sites
(5, 5)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC8 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
LEU A:121 , GLY A:125 , HIS A:126 , LEU A:127 , SER A:175 , ASN A:347 , SER A:355 , PRO A:356 , PHE A:357 , HOH A:664 , HOH A:694 , HOH A:787 , HOH A:859 , PLG A:1001 , GLU B:57 , TYR B:64 , TYR B:65 , PHE B:257 , HOH B:530 , HOH B:961 , SER D:245 , GLU D:246 , GLU D:247
BINDING SITE FOR RESIDUE FFO A 1002
2
AC5
SOFTWARE
SER C:35 , SER C:97 , GLY C:98 , SER C:99 , HIS C:126 , PHE C:174 , SER C:175 , ASP C:200 , ALA C:202 , HIS C:203 , THR C:226 , HIS C:228 , LYS C:229 , ARG C:363 , FFO C:3002 , TYR D:55 , TYR D:65 , GLY D:262 , GLY D:263 , HOH D:504
BINDING SITE FOR RESIDUE PLG C 3001
3
AC6
SOFTWARE
SER B:245 , GLU B:246 , GLU B:247 , LEU C:121 , GLY C:125 , HIS C:126 , LEU C:127 , SER C:175 , ASN C:347 , SER C:355 , PRO C:356 , PHE C:357 , HOH C:656 , PLG C:3001 , GLU D:57 , TYR D:64 , TYR D:65 , PHE D:257
BINDING SITE FOR RESIDUE FFO C 3002
4
AC7
SOFTWARE
TYR C:55 , TYR C:65 , GLY C:262 , GLY C:263 , HOH C:505 , SER D:35 , SER D:97 , GLY D:98 , SER D:99 , HIS D:126 , PHE D:174 , SER D:175 , ASP D:200 , ALA D:202 , HIS D:203 , THR D:226 , HIS D:228 , LYS D:229 , ARG D:363 , FFO D:4002
BINDING SITE FOR RESIDUE PLG D 4001
5
AC8
SOFTWARE
GLU C:57 , TYR C:64 , TYR C:65 , PHE C:257 , HOH C:525 , LEU D:121 , GLY D:125 , HIS D:126 , LEU D:127 , SER D:175 , ASN D:347 , SER D:355 , PRO D:356 , PHE D:357 , HOH D:674 , HOH D:675 , HOH D:1027 , PLG D:4001
BINDING SITE FOR RESIDUE FFO D 4002
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: SHMT (C:221-237,D:221-237)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SHMT
PS00096
Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.
GLYA_ECOLI
221-237
2
-
-
C:221-237
D:221-237
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Exons
(0, 0)
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1dfoa_ (A:)
1b: SCOP_d1dfob_ (B:)
1c: SCOP_d1dfoc_ (C:)
1d: SCOP_d1dfod_ (D:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
GABA-aminotransferase-like
(167)
Protein domain
:
Serine hydroxymethyltransferase
(50)
Escherichia coli [TaxId: 562]
(2)
1a
d1dfoa_
A:
1b
d1dfob_
B:
1c
d1dfoc_
C:
1d
d1dfod_
D:
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1dfoA01 (A:40-280)
1b: CATH_1dfoB01 (B:40-280)
1c: CATH_1dfoC01 (C:40-280)
1d: CATH_1dfoD01 (D:40-280)
2a: CATH_1dfoA02 (A:281-417)
2b: CATH_1dfoB02 (B:281-417)
2c: CATH_1dfoC02 (C:281-417)
2d: CATH_1dfoD02 (D:281-417)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Escherichia coli. Organism_taxid: 562.
(56)
1a
1dfoA01
A:40-280
1b
1dfoB01
B:40-280
1c
1dfoC01
C:40-280
1d
1dfoD01
D:40-280
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Escherichia coli. Organism_taxid: 562.
(56)
2a
1dfoA02
A:281-417
2b
1dfoB02
B:281-417
2c
1dfoC02
C:281-417
2d
1dfoD02
D:281-417
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (272 KB)
Header - Asym.Unit
Biol.Unit 1 (136 KB)
Header - Biol.Unit 1
Biol.Unit 2 (135 KB)
Header - Biol.Unit 2
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