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1NVT
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Title
:
CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE (AROE OR MJ1084) IN COMPLEX WITH NADP+
Authors
:
A. K. Padyana, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
04 Feb 03 (Deposition) - 25 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Oxidoreductase
(Keyword Search:
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Reference
:
A. K. Padyana, S. K. Burley
Crystal Structure Of Shikimate 5-Dehydrogenase (Sdh) Bound To Nadp: Insights Into Function And Evolution
Structure V. 11 1005 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
1b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
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No.
Name
Count
Type
Full Name
1
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2
ZN
2
Ligand/Ion
ZINC ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:19 , ASN B:279 , ASP B:283
BINDING SITE FOR RESIDUE ZN A 290
2
AC2
SOFTWARE
GLU B:22 , HIS B:23 , ASP B:190 , ASP B:192
BINDING SITE FOR RESIDUE ZN B 291
3
AC3
SOFTWARE
GLY A:135 , ALA A:136 , GLY A:137 , ALA A:139 , ASN A:157 , ARG A:158 , THR A:159 , LYS A:162 , ALA A:200 , THR A:201 , PRO A:202 , ILE A:203 , MET A:205 , LEU A:229 , ILE A:230 , TYR A:231 , GLY A:252 , MET A:255 , LEU A:256 , HOH A:296 , HOH A:316 , HOH A:333 , ASN B:246 , LYS B:248
BINDING SITE FOR RESIDUE NAP A 288
4
AC4
SOFTWARE
ILE B:72 , GLY B:135 , ALA B:136 , GLY B:137 , GLY B:138 , ALA B:139 , ASN B:157 , ARG B:158 , THR B:159 , LYS B:162 , ALA B:200 , THR B:201 , PRO B:202 , ILE B:203 , MET B:205 , LEU B:229 , TYR B:231 , GLY B:252 , MET B:255 , LEU B:256
BINDING SITE FOR RESIDUE NAP B 289
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
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Exons
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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_d1nvta2 (A:1-110)
1b: SCOP_d1nvtb2 (B:1-110)
2a: SCOP_d1nvta1 (A:111-287)
2b: SCOP_d1nvtb1 (B:111-287)
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Protein Domains
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(
)
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
:
Shikimate 5-dehydrogenase AroE
(10)
Methanococcus jannaschii [TaxId: 2190]
(1)
1a
d1nvta2
A:1-110
1b
d1nvtb2
B:1-110
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
:
Shikimate 5-dehydrogenase AroE
(10)
Methanococcus jannaschii [TaxId: 2190]
(1)
2a
d1nvta1
A:111-287
2b
d1nvtb1
B:111-287
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1nvtA01 (A:1-109,A:252-287)
1b: CATH_1nvtB01 (B:1-109,B:252-287)
2a: CATH_1nvtA02 (A:110-251)
2b: CATH_1nvtB02 (B:110-251)
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Organisms
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)
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)
Methanocaldococcus jannaschii. Organism_taxid: 2190.
(1)
1a
1nvtA01
A:1-109,A:252-287
1b
1nvtB01
B:1-109,B:252-287
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Methanocaldococcus jannaschii. Organism_taxid: 2190.
(4)
2a
1nvtA02
A:110-251
2b
1nvtB02
B:110-251
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Shikimate_DH_1nvtB01 (B:118-253)
1b: PFAM_Shikimate_DH_1nvtB02 (B:118-253)
2a: PFAM_Shikimate_dh_N_1nvtB03 (B:16-98)
2b: PFAM_Shikimate_dh_N_1nvtB04 (B:16-98)
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Clans
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)
Clan
:
NADP_Rossmann
(1239)
Family
:
Shikimate_DH
(16)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(1)
1a
Shikimate_DH-1nvtB01
B:118-253
1b
Shikimate_DH-1nvtB02
B:118-253
Clan
:
no clan defined [family: Shikimate_dh_N]
(15)
Family
:
Shikimate_dh_N
(15)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(1)
2a
Shikimate_dh_N-1nvtB03
B:16-98
2b
Shikimate_dh_N-1nvtB04
B:16-98
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