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1NPD
Asym. Unit
Info
Asym.Unit (105 KB)
Biol.Unit 1 (99 KB)
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(1)
Title
:
X-RAY STRUCTURE OF SHIKIMATE DEHYDROGENASE COMPLEXED WITH NAD+ FROM E.COLI (YDIB) NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER24
Authors
:
J. Benach, A. P. Kuzin, I. Lee, B. Rost, Y. Chiang, T. B. Acton, G. T. Montelione, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date
:
17 Jan 03 (Deposition) - 28 Jan 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Benach, I. Lee, W. Edstrom, A. P. Kuzin, Y. Chiang, T. B. Acton, G. T. Montelione, J. F. Hunt
The 2. 3-A Crystal Structure Of The Shikimate 5-Dehydrogenase Orthologue Ydib From Escherichia Coli Suggests A Novel Catalytic Environment For An Nad-Dependent Dehydrogenase
J. Biol. Chem. V. 278 19176 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 24)
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)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MSE
22
Mod. Amino Acid
SELENOMETHIONINE
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:107 , GLY A:131 , ALA A:132 , GLY A:133 , GLY A:134 , ALA A:135 , ASN A:155 , ARG A:156 , ASP A:158 , PHE A:160 , LEU A:184 , GLY A:203 , THR A:204 , LYS A:205 , VAL A:206 , MSE A:208 , CYS A:232 , VAL A:233 , TYR A:234 , ASN A:235 , GLY A:255 , MSE A:258 , LEU A:259 , HOH A:3013 , HOH A:3320 , HOH A:3321
BINDING SITE FOR RESIDUE NAD A 300
2
AC2
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 , TYR B:234 , GLY B:255 , MSE B:258 , LEU B:259 , HOH B:3014 , HOH B:3106 , HOH B:3111 , HOH B:3127 , HOH B:3271
BINDING SITE FOR RESIDUE NAD B 300
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1npda2 (A:1-106)
1b: SCOP_d1npdb2 (B:1-106)
2a: SCOP_d1npda1 (A:107-287)
2b: SCOP_d1npdb1 (B:107-288)
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)
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)
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(
)
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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
d1npda2
A:1-106
1b
d1npdb2
B:1-106
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
d1npda1
A:107-287
2b
d1npdb1
B:107-288
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1npdB01 (B:2-104,B:254-288)
1b: CATH_1npdA01 (A:2-107,A:259-287)
2a: CATH_1npdA02 (A:108-257)
2b: CATH_1npdB02 (B:105-253)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
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.
(1)
1a
1npdB01
B:2-104,B:254-288
1b
1npdA01
A:2-107,A:259-287
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 562.
(49)
2a
1npdA02
A:108-257
2b
1npdB02
B:105-253
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Shikimate_DH_1npdB01 (B:114-230)
1b: PFAM_Shikimate_DH_1npdB02 (B:114-230)
2a: PFAM_Shikimate_dh_N_1npdB03 (B:12-94)
2b: PFAM_Shikimate_dh_N_1npdB04 (B:12-94)
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)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Shikimate_DH
(16)
Escherichia coli (strain K12)
(3)
1a
Shikimate_DH-1npdB01
B:114-230
1b
Shikimate_DH-1npdB02
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-1npdB03
B:12-94
2b
Shikimate_dh_N-1npdB04
B:12-94
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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