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1PWH
Asym. Unit
Info
Asym.Unit (204 KB)
Biol.Unit 1 (53 KB)
Biol.Unit 2 (53 KB)
Biol.Unit 3 (53 KB)
Biol.Unit 4 (53 KB)
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(1)
Title
:
RAT LIVER L-SERINE DEHYDRATASE- COMPLEX WITH PYRIDOXYL-(O-METHYL-SERINE)-5-MONOPHOSPHATE
Authors
:
T. Yamada, J. Komoto, Y. Takata, H. Ogawa, F. Takusagawa
Date
:
01 Jul 03 (Deposition) - 02 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Rat Liver, L-Serine Dehydratase, Complex, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Yamada, J. Komoto, Y. Takata, H. Ogawa, H. C. Pitot, F. Takusagawa
Crystal Structure Of Serine Dehydratase From Rat Liver.
Biochemistry V. 42 12854 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHO... (PLVa)
2b: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHO... (PLVb)
2c: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHO... (PLVc)
2d: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHO... (PLVd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
K
4
Ligand/Ion
POTASSIUM ION
2
PLV
4
Ligand/Ion
N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-O-METHYL-L-SERINE
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:167 , GLY A:168 , GLU A:194 , ALA A:198 , SER A:200 , LEU A:223
BINDING SITE FOR RESIDUE K A 332
2
AC2
SOFTWARE
VAL B:167 , GLY B:168 , GLU B:194 , ALA B:198 , SER B:200 , LEU B:223
BINDING SITE FOR RESIDUE K B 333
3
AC3
SOFTWARE
VAL C:167 , GLY C:168 , GLU C:194 , ALA C:198 , SER C:200 , LEU C:223
BINDING SITE FOR RESIDUE K C 334
4
AC4
SOFTWARE
VAL D:167 , GLY D:168 , GLU D:194 , ALA D:198 , SER D:200 , LEU D:223
BINDING SITE FOR RESIDUE K D 335
5
AC5
SOFTWARE
PHE A:40 , LYS A:41 , SER A:64 , ALA A:65 , ASN A:67 , ALA A:68 , PRO A:135 , PHE A:136 , SER A:166 , VAL A:167 , GLY A:168 , GLY A:169 , GLY A:170 , GLY A:171 , LEU A:172 , LYS A:221 , ALA A:222 , GLY A:224 , CYS A:303 , GLY A:304 , HOH A:334 , HOH A:350 , HOH A:356
BINDING SITE FOR RESIDUE PLV A 328
6
AC6
SOFTWARE
PHE B:40 , LYS B:41 , SER B:64 , ALA B:65 , ASN B:67 , ALA B:68 , PHE B:136 , SER B:166 , GLY B:168 , GLY B:169 , GLY B:170 , GLY B:171 , LEU B:172 , LYS B:221 , ALA B:222 , GLY B:224 , CYS B:303 , HOH B:334 , HOH B:336 , HOH B:347
BINDING SITE FOR RESIDUE PLV B 329
7
AC7
SOFTWARE
PHE C:40 , LYS C:41 , SER C:64 , ALA C:65 , ASN C:67 , ALA C:68 , PRO C:135 , PHE C:136 , SER C:166 , VAL C:167 , GLY C:168 , GLY C:169 , GLY C:170 , GLY C:171 , LEU C:172 , LYS C:221 , ALA C:222 , GLY C:224 , CYS C:303 , HOH C:337 , HOH C:339
BINDING SITE FOR RESIDUE PLV C 330
8
AC8
SOFTWARE
PHE D:40 , LYS D:41 , SER D:64 , ALA D:65 , ASN D:67 , ALA D:68 , PHE D:136 , SER D:166 , VAL D:167 , GLY D:168 , GLY D:169 , GLY D:170 , GLY D:171 , LEU D:172 , LYS D:221 , ALA D:222 , GLY D:224 , CYS D:303 , HOH D:336 , HOH D:339
BINDING SITE FOR RESIDUE PLV D 331
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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: DEHYDRATASE_SER_THR (A:32-45,B:32-45,C:32-45,D:32-45)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DEHYDRATASE_SER_THR
PS00165
Serine/threonine dehydratases pyridoxal-phosphate attachment site.
SDHL_RAT
32-45
4
A:32-45
B:32-45
C:32-45
D:32-45
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Exons
(0, 0)
Info
All Exons
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1pwha_ (A:)
1b: SCOP_d1pwhb_ (B:)
1c: SCOP_d1pwhc_ (C:)
1d: SCOP_d1pwhd_ (D:)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(165)
Superfamily
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(165)
Family
:
Tryptophan synthase beta subunit-like PLP-dependent enzymes
(120)
Protein domain
:
L-serine dehydratase
(3)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(2)
1a
d1pwha_
A:
1b
d1pwhb_
B:
1c
d1pwhc_
C:
1d
d1pwhd_
D:
[
close SCOP info
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1pwhA01 (A:1-43,A:136-327)
1b: CATH_1pwhA02 (A:44-135)
1c: CATH_1pwhB02 (B:44-135)
1d: CATH_1pwhC02 (C:44-135)
1e: CATH_1pwhD02 (D:44-135)
1f: CATH_1pwhB01 (B:1-43,B:136-327)
1g: CATH_1pwhC01 (C:1-43,C:136-327)
1h: CATH_1pwhD01 (D:1-43,D:136-327)
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Organisms
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)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1100, no name defined]
(77)
Norway rat (Rattus norvegicus)
(2)
1a
1pwhA01
A:1-43,A:136-327
1b
1pwhA02
A:44-135
1c
1pwhB02
B:44-135
1d
1pwhC02
C:44-135
1e
1pwhD02
D:44-135
1f
1pwhB01
B:1-43,B:136-327
1g
1pwhC01
C:1-43,C:136-327
1h
1pwhD01
D:1-43,D:136-327
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_PALP_1pwhD01 (D:5-304)
1b: PFAM_PALP_1pwhD02 (D:5-304)
1c: PFAM_PALP_1pwhD03 (D:5-304)
1d: PFAM_PALP_1pwhD04 (D:5-304)
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Clan
:
no clan defined [family: PALP]
(67)
Family
:
PALP
(67)
Rattus norvegicus (Rat)
(2)
1a
PALP-1pwhD01
D:5-304
1b
PALP-1pwhD02
D:5-304
1c
PALP-1pwhD03
D:5-304
1d
PALP-1pwhD04
D:5-304
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Asymmetric Unit 1
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Asym.Unit (204 KB)
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