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2RKB
Biol. Unit 2
Info
Asym.Unit (250 KB)
Biol.Unit 1 (101 KB)
Biol.Unit 2 (100 KB)
Biol.Unit 3 (101 KB)
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(1)
Title
:
SERINE DEHYDRATASE LIKE-1 FROM HUMAN CANCER CELLS
Authors
:
T. Yamada, J. Komoto, T. Kasuya, H. Mori, H. Ogawa, F. Takusagawa
Date
:
16 Oct 07 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E (2x)
Keywords
:
Serine Dehydratase, Plp Bound Enzyme, Enzyme Found In Human Cancer Cells, Lyase, Pyridoxal Phosphate
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Yamada, J. Komoto, T. Kasuya, Y. Takata, H. Ogawa, H. Mori, F. Takusagawa
A Catalytic Mechanism That Explains A Low Catalytic Activit Of Serine Dehydratase Like-1 From Human Cancer Cells: Crystal Structure And Site-Directed Mutagenesis Studies.
Biochim. Biophys. Acta V. 1780 809 2008
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
2b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
2c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
2d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
2e: PYRIDOXAL-5'-PHOSPHATE (PLPe)
View:
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Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
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Sites
(4, 4)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
GLY C:174 , GLU C:200 , ALA C:204 , CYS C:206 , LEU C:229
BINDING SITE FOR RESIDUE K C 401
2
AC4
SOFTWARE
GLY D:174 , GLU D:200 , ALA D:204 , CYS D:206 , LEU D:229
BINDING SITE FOR RESIDUE K D 401
3
AC8
SOFTWARE
PHE C:47 , LYS C:48 , ASN C:74 , PHE C:142 , GLY C:174 , GLY C:175 , GLY C:176 , GLY C:177 , LEU C:178 , SER C:228 , CYS C:309 , HOH C:416 , HOH C:427
BINDING SITE FOR RESIDUE PLP C 400
4
AC9
SOFTWARE
PHE D:47 , LYS D:48 , ASN D:74 , PHE D:142 , GLY D:174 , GLY D:175 , GLY D:176 , GLY D:177 , LEU D:178 , SER D:228 , CYS D:309
BINDING SITE FOR RESIDUE PLP D 400
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: DEHYDRATASE_SER_THR (C:39-52,D:39-52)
;
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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.
SDSL_HUMAN
39-52
2
-
-
C:39-52
D:39-52
-
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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, 5)
Info
All SCOP Domains
1a: SCOP_d2rkba_ (A:)
1b: SCOP_d2rkbb_ (B:)
1c: SCOP_d2rkbc_ (C:)
1d: SCOP_d2rkbd_ (D:)
1e: SCOP_d2rkbe_ (E:)
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Protein Domains
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(
)
Organisms
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)
(
)
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
:
automated matches
(45)
Protein domain
:
automated matches
(45)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d2rkba_
A:
1b
d2rkbb_
B:
1c
d2rkbc_
C:
1d
d2rkbd_
D:
1e
d2rkbe_
E:
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CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_2rkbA01 (A:11-50,A:142-328)
1b: CATH_2rkbB01 (B:11-50,B:142-328)
1c: CATH_2rkbC01 (C:11-50,C:142-328)
1d: CATH_2rkbD01 (D:11-50,D:142-328)
1e: CATH_2rkbE01 (E:11-50,E:142-328)
1f: CATH_2rkbA02 (A:51-141)
1g: CATH_2rkbB02 (B:51-141)
1h: CATH_2rkbC02 (C:51-141)
1i: CATH_2rkbD02 (D:51-141)
1j: CATH_2rkbE02 (E:51-141)
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)
Organisms
(
)
(
)
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)
Human (Homo sapiens)
(4)
1a
2rkbA01
A:11-50,A:142-328
1b
2rkbB01
B:11-50,B:142-328
1c
2rkbC01
C:11-50,C:142-328
1d
2rkbD01
D:11-50,D:142-328
1e
2rkbE01
E:11-50,E:142-328
1f
2rkbA02
A:51-141
1g
2rkbB02
B:51-141
1h
2rkbC02
C:51-141
1i
2rkbD02
D:51-141
1j
2rkbE02
E:51-141
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Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_PALP_2rkbE01 (E:11-310)
1b: PFAM_PALP_2rkbE02 (E:11-310)
1c: PFAM_PALP_2rkbE03 (E:11-310)
1d: PFAM_PALP_2rkbE04 (E:11-310)
1e: PFAM_PALP_2rkbE05 (E:11-310)
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Clan
:
no clan defined [family: PALP]
(67)
Family
:
PALP
(67)
Homo sapiens (Human)
(6)
1a
PALP-2rkbE01
E:11-310
1b
PALP-2rkbE02
E:11-310
1c
PALP-2rkbE03
E:11-310
1d
PALP-2rkbE04
E:11-310
1e
PALP-2rkbE05
E:11-310
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