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1VFH
Biol. Unit 1
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Asym.Unit (65 KB)
Biol.Unit 1 (120 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM D-CYCLOSERINE PRODUCING STREPTOMYCES LAVENDULAE
Authors
:
M. Noda, Y. Matoba, T. Kumagai, M. Sugiyama
Date
:
13 Apr 04 (Deposition) - 14 Sep 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Tim-Barrel, Greek-Key Motief, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Noda, Y. Matoba, T. Kumagai, M. Sugiyama
Structural Evidence That Alanine Racemase From A D-Cycloserine-Producing Microorganism Exhibits Resistance T Its Own Product.
J. Biol. Chem. V. 279 46153 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
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No.
Name
Count
Type
Full Name
1
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
2
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
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Sites
(1, 1)
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All Sites
1: AC1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:38 , TYR A:42 , TRP A:84 , ARG A:136 , TRP A:166 , HIS A:168 , SER A:209 , PRO A:210 , ARG A:224 , GLY A:226 , LEU A:227 , TYR A:361 , HOH A:508 , HOH A:526
BINDING SITE FOR RESIDUE PLP A 401
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
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SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1vfha1 (A:3-12,A:250-384)
2a: SCOP_d1vfha2 (A:13-249)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Domain of alpha and beta subunits of F1 ATP synthase-like
(89)
Superfamily
:
Alanine racemase C-terminal domain-like
(25)
Family
:
Alanine racemase
(12)
Protein domain
:
Alanine racemase
(12)
Streptomyces lavendulae [TaxId: 1914]
(3)
1a
d1vfha1
A:3-12,A:250-384
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLP-binding barrel
(27)
Family
:
Alanine racemase-like, N-terminal domain
(25)
Protein domain
:
Alanine racemase
(12)
Streptomyces lavendulae [TaxId: 1914]
(3)
2a
d1vfha2
A:13-249
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1vfhA02 (A:14-229)
2a: CATH_1vfhA01 (A:3-13,A:249-384)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Alanine racemase
(53)
Streptomyces lavendulae. Organism_taxid: 1914.
(3)
1a
1vfhA02
A:14-229
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Homologous Superfamily
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Streptomyces lavendulae. Organism_taxid: 1914.
(3)
2a
1vfhA01
A:3-13,A:249-384
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Ala_racemase_N_1vfhA01 (A:12-234)
2a: PFAM_Ala_racemase_C_1vfhA02 (A:249-376)
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Clan
:
TIM_barrel
(694)
Family
:
Ala_racemase_N
(19)
Streptomyces lavendulae subsp. lavendulae
(3)
1a
Ala_racemase_N-1vfhA01
A:12-234
Clan
:
no clan defined [family: Ala_racemase_C]
(18)
Family
:
Ala_racemase_C
(18)
Streptomyces lavendulae subsp. lavendulae
(3)
2a
Ala_racemase_C-1vfhA02
A:249-376
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