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2VD8
Asym. Unit
Info
Asym.Unit (158 KB)
Biol.Unit 1 (149 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM BACILLUS ANTHRACIS (BA0252)
Authors
:
K. Au, J. Ren, T. S. Walter, K. Harlos, J. E. Nettleship, R. J. Owens, D. I. R. M. Esnouf, Oxford Protein Production Facility (Oppf), Struct Proteomics In Europe (Spine)
Date
:
01 Oct 07 (Deposition) - 20 May 08 (Release) - 06 May 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.47
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Pyridoxal 5'-Phosphate, Peptidoglycan Synthesis, Plp, Oppf, L-Alanine, Isomerase, D- Alanine, Pyridoxal Phosphate, Structural Genomics, Alanine Racemase, Spore Germination, Oxford Protein Production Facility, Structural Proteomics In Europe (Spine)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Au, J. Ren, T. S. Walter, K. Harlos, J. E. Nettleship, R. J. Owens, D. I. Stuart, R. M. Esnouf
Structures Of An Alanine Racemase From Bacillus Anthracis (Ba0252) In The Presence And Absence Of (R)-1-Aminoethylphosphonic Acid (L-Ala-P).
Acta Crystallogr. , Sect. F V. 64 327 2008
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Hetero Components
(4, 45)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: N-DIMETHYL-LYSINE (MLYa)
3aa: N-DIMETHYL-LYSINE (MLYaa)
3ab: N-DIMETHYL-LYSINE (MLYab)
3ac: N-DIMETHYL-LYSINE (MLYac)
3ad: N-DIMETHYL-LYSINE (MLYad)
3ae: N-DIMETHYL-LYSINE (MLYae)
3af: N-DIMETHYL-LYSINE (MLYaf)
3ag: N-DIMETHYL-LYSINE (MLYag)
3ah: N-DIMETHYL-LYSINE (MLYah)
3ai: N-DIMETHYL-LYSINE (MLYai)
3aj: N-DIMETHYL-LYSINE (MLYaj)
3b: N-DIMETHYL-LYSINE (MLYb)
3c: N-DIMETHYL-LYSINE (MLYc)
3d: N-DIMETHYL-LYSINE (MLYd)
3e: N-DIMETHYL-LYSINE (MLYe)
3f: N-DIMETHYL-LYSINE (MLYf)
3g: N-DIMETHYL-LYSINE (MLYg)
3h: N-DIMETHYL-LYSINE (MLYh)
3i: N-DIMETHYL-LYSINE (MLYi)
3j: N-DIMETHYL-LYSINE (MLYj)
3k: N-DIMETHYL-LYSINE (MLYk)
3l: N-DIMETHYL-LYSINE (MLYl)
3m: N-DIMETHYL-LYSINE (MLYm)
3n: N-DIMETHYL-LYSINE (MLYn)
3o: N-DIMETHYL-LYSINE (MLYo)
3p: N-DIMETHYL-LYSINE (MLYp)
3q: N-DIMETHYL-LYSINE (MLYq)
3r: N-DIMETHYL-LYSINE (MLYr)
3s: N-DIMETHYL-LYSINE (MLYs)
3t: N-DIMETHYL-LYSINE (MLYt)
3u: N-DIMETHYL-LYSINE (MLYu)
3v: N-DIMETHYL-LYSINE (MLYv)
3w: N-DIMETHYL-LYSINE (MLYw)
3x: N-DIMETHYL-LYSINE (MLYx)
3y: N-DIMETHYL-LYSINE (MLYy)
3z: N-DIMETHYL-LYSINE (MLYz)
4a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
4b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
3
Ligand/Ion
CHLORIDE ION
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
MLY
36
Mod. Amino Acid
N-DIMETHYL-LYSINE
4
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:161 , HOH A:2271 , HOH A:2273 , HOH A:2274 , HOH B:2218 , HOH B:2221
BINDING SITE FOR RESIDUE MG B1001
2
AC2
SOFTWARE
HOH A:2455 , GLY B:306 , ASP B:342 , GLU B:343 , HOH B:2406 , HOH B:2410
BINDING SITE FOR RESIDUE MG B1002
3
AC3
SOFTWARE
HOH A:2158 , HOH A:2159 , HOH A:2160 , HOH A:2404 , HOH A:2405
BINDING SITE FOR RESIDUE MG B1003
4
AC4
SOFTWARE
ASP A:17 , HOH A:2033 , HOH A:2034 , HOH A:2035 , HOH A:2539 , HOH B:2388
BINDING SITE FOR RESIDUE MG A1390
5
AC5
SOFTWARE
ARG A:144 , GLN A:216 , HOH A:2247 , HOH A:2249
BINDING SITE FOR RESIDUE CL A1391
6
AC6
SOFTWARE
ASN A:131 , ARG A:138
BINDING SITE FOR RESIDUE CL A1392
7
AC7
SOFTWARE
ASN B:131 , ARG B:138
BINDING SITE FOR RESIDUE CL B1390
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2vd8A02 (A:16-229)
1b: CATH_2vd8B02 (B:16-229)
2a: CATH_2vd8B01 (B:4-15,B:249-389)
2b: CATH_2vd8A01 (A:3-15,A:249-389)
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(
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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)
Bacillus anthracis. Organism_taxid: 198094. Strain: ames.
(2)
1a
2vd8A02
A:16-229
1b
2vd8B02
B:16-229
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)
Bacillus anthracis. Organism_taxid: 198094. Strain: ames.
(2)
2a
2vd8B01
B:4-15,B:249-389
2b
2vd8A01
A:3-15,A:249-389
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Ala_racemase_N_2vd8B01 (B:14-234)
1b: PFAM_Ala_racemase_N_2vd8B02 (B:14-234)
2a: PFAM_Ala_racemase_C_2vd8B03 (B:249-374)
2b: PFAM_Ala_racemase_C_2vd8B04 (B:249-374)
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Clans
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(
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Families
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(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
Ala_racemase_N
(19)
Bacillus anthracis
(2)
1a
Ala_racemase_N-2vd8B01
B:14-234
1b
Ala_racemase_N-2vd8B02
B:14-234
Clan
:
no clan defined [family: Ala_racemase_C]
(18)
Family
:
Ala_racemase_C
(18)
Bacillus anthracis
(2)
2a
Ala_racemase_C-2vd8B03
B:249-374
2b
Ala_racemase_C-2vd8B04
B:249-374
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Asymmetric Unit 1
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Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (158 KB)
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