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2FDF
Asym. Unit
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Asym.Unit (44 KB)
Biol.Unit 1 (40 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ALKB IN COMPLEX WITH CO(II), 2-OXOGLUTARATE, AND METHYLATED TRINUCLEOTIDE T-MEA-T
Authors
:
B. Yu, J. Benach, W. C. Edstrom, B. R. Gibney, J. F. Hunt, Northeast Stru Genomics Consortium (Nesg)
Date
:
13 Dec 05 (Deposition) - 21 Feb 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Beta Jellyroll, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Oxidoreductase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Yu, W. C. Edstrom, J. Benach, Y. Hamuro, P. C. Weber, B. R. Gibney, J. F. Hunt
Crystal Structures Of Catalytic Complexes Of The Oxidative Dna/Rna Repair Enzyme Alkb.
Nature V. 439 879 2006
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: 2-OXOGLUTARIC ACID (AKGa)
2a: COBALT (II) ION (COa)
3a: 1N-METHYLADENOSINE-5'-MONOPHOSPHAT... (MA7a)
View:
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No.
Name
Count
Type
Full Name
1
AKG
1
Ligand/Ion
2-OXOGLUTARIC ACID
2
CO
1
Ligand/Ion
COBALT (II) ION
3
MA7
1
Mod. Nucleotide
1N-METHYLADENOSINE-5'-MONOPHOSPHATE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:131 , ASP A:133 , HIS A:187 , AKG A:400 , HOH A:697
BINDING SITE FOR RESIDUE CO A 300
2
AC2
SOFTWARE
LEU A:118 , ASN A:120 , TYR A:122 , LEU A:128 , HIS A:131 , ASP A:133 , HIS A:187 , ILE A:189 , ARG A:204 , ASN A:206 , THR A:208 , ARG A:210 , CO A:300 , HOH A:625 , MA7 B:502
BINDING SITE FOR RESIDUE AKG A 400
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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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: FE2OG_OXY (A:113-213)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FE2OG_OXY
PS51471
Fe(2+) 2-oxoglutarate dioxygenase domain profile.
ALKB_ECOLI
113-213
1
A:113-213
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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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2fdfa_ (A:)
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Protein Domains
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)
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)
Organisms
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)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
Clavaminate synthase-like
(197)
Family
:
AlkB-like
(29)
Protein domain
:
Alkylated DNA repair protein AlkB
(10)
Escherichia coli [TaxId: 562]
(10)
1a
d2fdfa_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2fdfA00 (A:15-214)
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Organisms
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)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Clavaminate synthase-like domains
(16)
[unclassified]
(6)
1a
2fdfA00
A:15-214
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Pfam Domains
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Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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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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select non-helix/non-sheet protein parts
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