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1O9B
Biol. Unit 2
Info
Asym.Unit (102 KB)
Biol.Unit 1 (50 KB)
Biol.Unit 2 (49 KB)
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(1)
Title
:
QUINATE/SHIKIMATE DEHYDROGENASE YDIB COMPLEXED WITH NADH
Authors
:
G. Michel, M. Cygler
Date
:
12 Dec 02 (Deposition) - 01 Feb 03 (Release) - 30 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Oxidoreductase, Quinate, Shikimate, Nad, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
G. Michel, A. W. Roszak, V. Sauve, J. Mclean, A. Matte, J. R. Coggins, M. Cygler, A. J. Lapthorn
Structures Of Shikimate Dehydrogenase Aroe And Its Paralog Ydib: A Common Structural Framework For Different Activities
J. Biol. Chem. V. 278 19463 2003
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
2a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
2b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
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Label:
No.
Name
Count
Type
Full Name
1
MSE
10
Mod. Amino Acid
SELENOMETHIONINE
2
NAI
1
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3
PO4
2
Ligand/Ion
PHOSPHATE ION
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Sites
(3, 3)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
SER B:67 , LYS B:71 , ASP B:107 , NAI B:301 , HOH B:2065
BINDING SITE FOR RESIDUE PO4 B 302
2
AC5
SOFTWARE
MSE B:68 , PRO B:69 , ASN B:70 , LYS B:71 , GLN B:72 , HOH B:2062 , HOH B:2066
BINDING SITE FOR RESIDUE PO4 B 303
3
AC7
SOFTWARE
ASP B:107 , ALA B:132 , GLY B:133 , GLY B:134 , ALA B:135 , ASN B:155 , ARG B:156 , ASP B:158 , PHE B:160 , GLY B:203 , THR B:204 , LYS B:205 , VAL B:206 , MSE B:208 , CYS B:232 , VAL B:233 , TYR B:234 , GLY B:255 , MSE B:258 , LEU B:259 , PO4 B:302 , HOH B:2044 , HOH B:2062 , HOH B:2063 , HOH B:2064
BINDING SITE FOR RESIDUE NAI B 301
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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
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Exons
(0, 0)
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Note:
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1o9ba2 (A:7-106)
1b: SCOP_d1o9bb2 (B:7-106)
2a: SCOP_d1o9ba1 (A:107-287)
2b: SCOP_d1o9bb1 (B:107-287)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Shikimate dehydrogenase-like
(14)
Protein domain
:
Putative shikimate dehydrogenase YdiB
(3)
Escherichia coli [TaxId: 562]
(3)
1a
d1o9ba2
A:7-106
1b
d1o9bb2
B:7-106
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Putative shikimate dehydrogenase YdiB
(3)
Escherichia coli [TaxId: 562]
(3)
2a
d1o9ba1
A:107-287
2b
d1o9bb1
B:107-287
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1o9bA01 (A:7-104,A:254-287)
1b: CATH_1o9bB01 (B:7-107,B:259-287)
2a: CATH_1o9bB02 (B:108-257)
2b: CATH_1o9bA02 (A:105-253)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Leucine Dehydrogenase; Chain A, domain 1
(52)
Homologous Superfamily
:
Leucine Dehydrogenase, chain A, domain 1
(52)
Escherichia coli. Organism_taxid: 562. Strain: mc1061 p3.
(1)
1a
1o9bA01
A:7-104,A:254-287
1b
1o9bB01
B:7-107,B:259-287
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 562. Strain: mc1061 p3.
(1)
2a
1o9bB02
B:108-257
2b
1o9bA02
A:105-253
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Shikimate_DH_1o9bB01 (B:114-230)
1b: PFAM_Shikimate_DH_1o9bB02 (B:114-230)
2a: PFAM_Shikimate_dh_N_1o9bB03 (B:12-94)
2b: PFAM_Shikimate_dh_N_1o9bB04 (B:12-94)
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)
Clan
:
NADP_Rossmann
(1239)
Family
:
Shikimate_DH
(16)
Escherichia coli (strain K12)
(3)
1a
Shikimate_DH-1o9bB01
B:114-230
1b
Shikimate_DH-1o9bB02
B:114-230
Clan
:
no clan defined [family: Shikimate_dh_N]
(15)
Family
:
Shikimate_dh_N
(15)
Escherichia coli (strain K12)
(3)
2a
Shikimate_dh_N-1o9bB03
B:12-94
2b
Shikimate_dh_N-1o9bB04
B:12-94
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Chain B
Asymmetric Unit 1
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Asym.Unit (102 KB)
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