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1VI2
Asym. Unit
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Asym.Unit (103 KB)
Biol.Unit 1 (96 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SHIKIMATE-5-DEHYDROGENASE WITH NAD
Authors
:
Structural Genomix
Date
:
01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Structural Genomics, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
(for further references see the
PDB file header
)
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Hetero Components
(3, 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)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
SO4
2
Ligand/Ion
SULFATE ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:67 , MSE A:68 , PRO A:69 , ASN A:70 , LYS A:71 , GLN A:72
BINDING SITE FOR RESIDUE SO4 A 299
2
AC2
SOFTWARE
MSE B:68 , PRO B:69 , ASN B:70 , LYS B:71 , GLN B:72 , HOH B:316 , HOH B:356
BINDING SITE FOR RESIDUE SO4 B 299
3
AC3
SOFTWARE
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 , GLY A:203 , THR A:204 , LYS A:205 , VAL A:206 , MSE A:208 , CYS A:232 , VAL A:233 , TYR A:234 , GLY A:255 , MSE A:258 , LEU A:259 , HOH A:313 , HOH A:327 , HOH A:328 , HOH A:329 , HOH A:334 , HOH A:398 , HOH A:399 , HOH A:402
BINDING SITE FOR RESIDUE NAD A 300
4
AC4
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 , HOH B:304 , HOH B:309 , HOH B:315 , HOH B:335 , HOH B:351 , HOH B:394 , HOH B:400 , HOH B:409 , HOH B:425
BINDING SITE FOR RESIDUE NAD B 300
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SAPs(SNPs)/Variants
(0, 0)
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(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_d1vi2a2 (A:5-106)
1b: SCOP_d1vi2b2 (B:6-106)
2a: SCOP_d1vi2a1 (A:107-288)
2b: SCOP_d1vi2b1 (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
d1vi2a2
A:5-106
1b
d1vi2b2
B:6-106
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
d1vi2a1
A:107-288
2b
d1vi2b1
B:107-287
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1vi2A01 (A:5-107,A:259-288)
1b: CATH_1vi2B01 (B:6-107,B:259-287)
2a: CATH_1vi2A02 (A:108-257)
2b: CATH_1vi2B02 (B:108-257)
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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.
(2)
1a
1vi2A01
A:5-107,A:259-288
1b
1vi2B01
B:6-107,B:259-287
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 562.
(48)
2a
1vi2A02
A:108-257
2b
1vi2B02
B:108-257
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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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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Asym.Unit (103 KB)
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Header - Biol.Unit 1
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