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2BI9
Asym. Unit
Info
Asym.Unit (134 KB)
Biol.Unit 1 (129 KB)
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(1)
Title
:
RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE F)
Authors
:
A. P. Dubnovitsky, R. B. G. Ravelli, A. N. Popov, A. C. Papageorgiou
Date
:
20 Jan 05 (Deposition) - 19 May 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.73
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transferase, Aminotransferase, Pyridoxal-5'-Phosphate, Radiation Damage
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. P. Dubnovitsky, R. B. G. Ravelli, A. N. Popov, A. C. Papageorgiou
Strain Relief At The Active Site Of Phosphoserine Aminotransferase Induced By Radiation Damage.
Protein Sci. V. 14 1498 2005
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Hetero Components
(5, 14)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
5a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
5b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
CL
4
Ligand/Ion
CHLORIDE ION
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
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Sites
(14, 14)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:256 , HOH A:2177 , HOH A:2181 , HOH A:2182 , GLU B:51 , HOH B:2064
BINDING SITE FOR RESIDUE MG A1362
02
AC2
SOFTWARE
ASP A:344 , HOH A:2260 , ASP B:66 , HOH B:2084 , HOH B:2085 , HOH B:2181
BINDING SITE FOR RESIDUE MG A1363
03
AC3
SOFTWARE
SER A:101 , TRP A:102 , ASN A:151 , THR A:152 , ILE A:153 , TYR A:154 , HOH A:2123
BINDING SITE FOR RESIDUE CL A1364
04
AC4
SOFTWARE
TRP A:102 , ARG A:334 , HOH A:2008
BINDING SITE FOR RESIDUE CL A1365
05
AC5
SOFTWARE
HOH A:2200 , HOH A:2202 , HOH B:2110 , HOH B:2242 , HOH B:2246 , HOH B:2247
BINDING SITE FOR RESIDUE MG B1362
06
AC6
SOFTWARE
ASP B:256 , HOH B:2215 , HOH B:2220 , HOH B:2222
BINDING SITE FOR RESIDUE MG B1363
07
AC7
SOFTWARE
SER B:101 , TRP B:102 , ASN B:151 , THR B:152 , ILE B:153
BINDING SITE FOR RESIDUE CL B1364
08
AC8
SOFTWARE
TRP B:102 , ILE B:153 , ARG B:334 , HOH B:2013 , HOH B:2293
BINDING SITE FOR RESIDUE CL B1365
09
AC9
SOFTWARE
GLY A:75 , ALA A:76 , SER A:77 , TRP A:102 , THR A:152 , ASP A:172 , SER A:174 , GLN A:195 , LYS A:196 , HOH A:2271 , HOH A:2272 , ASN B:237 , THR B:238 , HOH B:2206
BINDING SITE FOR RESIDUE PLP A1361
10
BC1
SOFTWARE
ASP A:279 , LYS A:291 , HOH A:2273 , HOH A:2274 , GLU B:269 , ILE B:343 , HOH B:2236
BINDING SITE FOR RESIDUE 1PE A1366
11
BC2
SOFTWARE
ASN A:237 , THR A:238 , HOH A:2170 , GLY B:75 , ALA B:76 , SER B:77 , PHE B:80 , TRP B:102 , THR B:152 , ASP B:172 , SER B:174 , GLN B:195 , LYS B:196 , HOH B:2316 , HOH B:2317
BINDING SITE FOR RESIDUE PLP B1361
12
BC3
SOFTWARE
GLN A:159 , LYS A:291 , ARG A:294 , LEU A:296 , HOH A:2277
BINDING SITE FOR RESIDUE PEG A1367
13
BC4
SOFTWARE
GLU A:104 , LYS A:123
BINDING SITE FOR RESIDUE PEG A1368
14
BC5
SOFTWARE
GLN B:159 , TYR B:275 , LYS B:291 , GLY B:292 , ARG B:294 , LEU B:296 , HOH B:2260
BINDING SITE FOR RESIDUE PEG B1366
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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, 2)
Info
All PROSITE Patterns/Profiles
1: AA_TRANSFER_CLASS_5 (A:187-206,B:187-206)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRANSFER_CLASS_5
PS00595
Aminotransferases class-V pyridoxal-phosphate attachment site.
SERC_BACAO
188-207
2
A:187-206
B:187-206
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2bi9a_ (A:)
1b: SCOP_d2bi9b_ (B:)
View:
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Phosphoserine aminotransferase, PSAT
(17)
Bacillus alcalophilus [TaxId: 1445]
(12)
1a
d2bi9a_
A:
1b
d2bi9b_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2bi9A01 (A:16-257)
1b: CATH_2bi9B01 (B:16-257)
2a: CATH_2bi9A02 (A:258-360)
2b: CATH_2bi9B02 (B:258-360)
View:
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Architectures
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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)
Bacillus alcalophilus. Organism_taxid: 1445.
(10)
1a
2bi9A01
A:16-257
1b
2bi9B01
B:16-257
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Bacillus alcalophilus. Organism_taxid: 1445.
(10)
2a
2bi9A02
A:258-360
2b
2bi9B02
B:258-360
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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Asym.Unit (134 KB)
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