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1XCB
Biol. Unit 1
Info
Asym.Unit (235 KB)
Biol.Unit 1 (69 KB)
Biol.Unit 2 (68 KB)
Biol.Unit 3 (69 KB)
Biol.Unit 4 (67 KB)
Biol.Unit 5 (446 KB)
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(1)
Title
:
X-RAY STRUCTURE OF A REX-FAMILY REPRESSOR/NADH COMPLEX FROM THERMUS AQUATICUS
Authors
:
E. A. Sickmier, D. Brekasis, S. Paranawithana, J. B. Bonanno, S. K. Burley, M. S. Paget, C. L. Kielkopf, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
01 Sep 04 (Deposition) - 28 Sep 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G (2x)
Biol. Unit 5: A,B,C,D,E,F,G (2x)
Keywords
:
Redox-Sensing, Winged Helix, Rossmann Fold, Nicotinamide Adenine Dinucleotide, Nad, Rex, Thermus Aquaticus, New York Sgx Research Center For Structural Genomics, Nysgxrc, Structural Genomics, Psi, Protein Structure Initiative, Dna Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. A. Sickmier, D. Brekasis, S. Paranawithana, J. B. Bonanno, M. S. Paget, S. K. Burley, C. L. Kielkopf
X-Ray Structure Of A Rex-Family Repressor/Nadh Complex: Insights Into The Mechanism Of Redox Sensing
Structure V. 13 43 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
3e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
3f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
3g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
MSE
2
Mod. Amino Acid
SELENOMETHIONINE
3
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY B:139 , GLY G:139
BINDING SITE FOR RESIDUE CA B 212
2
AC4
SOFTWARE
VAL A:86 , GLY A:87 , MSE A:88 , GLY A:89 , ARG A:90 , LEU A:91 , ASP A:112 , VAL A:113 , ASP A:114 , LYS A:117 , THR A:147 , VAL A:148 , PRO A:149 , ALA A:152 , ALA A:156 , PHE A:171 , ALA A:172 , PRO A:173 , VAL A:187 , PHE A:189 , HIS B:27 , ALA B:94 , TYR B:98
BINDING SITE FOR RESIDUE NAD A 213
3
AC5
SOFTWARE
ALA A:94 , TYR A:98 , PHE A:189 , VAL B:86 , GLY B:87 , MSE B:88 , GLY B:89 , ARG B:90 , LEU B:91 , ASP B:112 , VAL B:113 , LYS B:117 , THR B:147 , VAL B:148 , PRO B:149 , ARG B:150 , ALA B:152 , PHE B:171 , PRO B:173 , VAL B:187 , PHE B:189
BINDING SITE FOR RESIDUE NAD B 213
4
AC8
SOFTWARE
PHE A:43 , ARG A:46 , GLY E:87 , MSE E:88 , GLY E:89 , ARG E:90 , LEU E:91 , ASP E:112 , VAL E:113 , ASP E:114 , LYS E:117 , THR E:147 , VAL E:148 , PRO E:149 , ARG E:150 , ALA E:152 , PHE E:171 , ALA E:172 , PRO E:173 , VAL E:187 , PHE E:189 , ALA F:94 , TYR F:98
BINDING SITE FOR RESIDUE NAD E 212
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SAPs(SNPs)/Variants
(0, 0)
Info
(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, 14)
Info
All SCOP Domains
1a: SCOP_d1xcba1 (A:4-77)
1b: SCOP_d1xcbb1 (B:4-77)
1c: SCOP_d1xcbc1 (C:4-77)
1d: SCOP_d1xcbd1 (D:4-77)
1e: SCOP_d1xcbe1 (E:4-77)
1f: SCOP_d1xcbf1 (F:4-77)
1g: SCOP_d1xcbg1 (G:4-77)
2a: SCOP_d1xcba2 (A:78-203)
2b: SCOP_d1xcbb2 (B:78-203)
2c: SCOP_d1xcbc2 (C:78-203)
2d: SCOP_d1xcbd2 (D:78-203)
2e: SCOP_d1xcbe2 (E:78-203)
2f: SCOP_d1xcbf2 (F:78-203)
2g: SCOP_d1xcbg2 (G:78-203)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Winged helix DNA-binding domain
(576)
Family
:
Transcriptional repressor Rex, N-terminal domain
(2)
Protein domain
:
Transcriptional repressor Rex, N-terminal domain
(2)
Thermus aquaticus [TaxId: 271]
(2)
1a
d1xcba1
A:4-77
1b
d1xcbb1
B:4-77
1c
d1xcbc1
C:4-77
1d
d1xcbd1
D:4-77
1e
d1xcbe1
E:4-77
1f
d1xcbf1
F:4-77
1g
d1xcbg1
G:4-77
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Transcriptional repressor Rex, C-terminal domain
(2)
Protein domain
:
Transcriptional repressor Rex, C-terminal domain
(2)
Thermus aquaticus [TaxId: 271]
(2)
2a
d1xcba2
A:78-203
2b
d1xcbb2
B:78-203
2c
d1xcbc2
C:78-203
2d
d1xcbd2
D:78-203
2e
d1xcbe2
E:78-203
2f
d1xcbf2
F:78-203
2g
d1xcbg2
G:78-203
[
close SCOP info
]
CATH Domains
(2, 14)
Info
all CATH domains
1a: CATH_1xcbF02 (F:74-207)
1b: CATH_1xcbA02 (A:74-206)
1c: CATH_1xcbB02 (B:74-206)
1d: CATH_1xcbD02 (D:74-205)
1e: CATH_1xcbC02 (C:74-204)
1f: CATH_1xcbE02 (E:74-203)
1g: CATH_1xcbG02 (G:74-203)
2a: CATH_1xcbA01 (A:2-73)
2b: CATH_1xcbC01 (C:2-73)
2c: CATH_1xcbE01 (E:2-73)
2d: CATH_1xcbF01 (F:3-73)
2e: CATH_1xcbD01 (D:4-73)
2f: CATH_1xcbB01 (B:4-73)
2g: CATH_1xcbG01 (G:4-73)
View:
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(
)
(
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Thermus aquaticus. Organism_taxid: 271.
(3)
1a
1xcbF02
F:74-207
1b
1xcbA02
A:74-206
1c
1xcbB02
B:74-206
1d
1xcbD02
D:74-205
1e
1xcbC02
C:74-204
1f
1xcbE02
E:74-203
1g
1xcbG02
G:74-203
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
Thermus aquaticus. Organism_taxid: 271.
(1)
2a
1xcbA01
A:2-73
2b
1xcbC01
C:2-73
2c
1xcbE01
E:2-73
2d
1xcbF01
F:3-73
2e
1xcbD01
D:4-73
2f
1xcbB01
B:4-73
2g
1xcbG01
G:4-73
[
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Pfam Domains
(0, 0)
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all PFAM domains
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