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2VD9
Asym. Unit
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Asym.Unit (154 KB)
Biol.Unit 1 (145 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM BACILLUS ANTHRACIS (BA0252) WITH BOUND L-ALA-P
Authors
:
K. Au, J. Ren, T. S. Walter, K. Harlos, J. E. Nettleship, R. J. Owens, D. I. Stuart, R. M. Esnouf, Oxford Protein Production Facility (Oppf), Structural Proteomics In Europe (Spine)
Date
:
01 Oct 07 (Deposition) - 20 May 08 (Release) - 08 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
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
(5, 46)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: (1S)-1-[((1E)-{3-HYDROXY-2-METHYL-... (EPCa)
2b: (1S)-1-[((1E)-{3-HYDROXY-2-METHYL-... (EPCb)
3a: {1-[(3-HYDROXY-METHYL-5-PHOSPHONOO... (IN5a)
3b: {1-[(3-HYDROXY-METHYL-5-PHOSPHONOO... (IN5b)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
5a: N-DIMETHYL-LYSINE (MLYa)
5aa: N-DIMETHYL-LYSINE (MLYaa)
5ab: N-DIMETHYL-LYSINE (MLYab)
5ac: N-DIMETHYL-LYSINE (MLYac)
5ad: N-DIMETHYL-LYSINE (MLYad)
5ae: N-DIMETHYL-LYSINE (MLYae)
5af: N-DIMETHYL-LYSINE (MLYaf)
5ag: N-DIMETHYL-LYSINE (MLYag)
5ah: N-DIMETHYL-LYSINE (MLYah)
5ai: N-DIMETHYL-LYSINE (MLYai)
5aj: N-DIMETHYL-LYSINE (MLYaj)
5b: N-DIMETHYL-LYSINE (MLYb)
5c: N-DIMETHYL-LYSINE (MLYc)
5d: N-DIMETHYL-LYSINE (MLYd)
5e: N-DIMETHYL-LYSINE (MLYe)
5f: N-DIMETHYL-LYSINE (MLYf)
5g: N-DIMETHYL-LYSINE (MLYg)
5h: N-DIMETHYL-LYSINE (MLYh)
5i: N-DIMETHYL-LYSINE (MLYi)
5j: N-DIMETHYL-LYSINE (MLYj)
5k: N-DIMETHYL-LYSINE (MLYk)
5l: N-DIMETHYL-LYSINE (MLYl)
5m: N-DIMETHYL-LYSINE (MLYm)
5n: N-DIMETHYL-LYSINE (MLYn)
5o: N-DIMETHYL-LYSINE (MLYo)
5p: N-DIMETHYL-LYSINE (MLYp)
5q: N-DIMETHYL-LYSINE (MLYq)
5r: N-DIMETHYL-LYSINE (MLYr)
5s: N-DIMETHYL-LYSINE (MLYs)
5t: N-DIMETHYL-LYSINE (MLYt)
5u: N-DIMETHYL-LYSINE (MLYu)
5v: N-DIMETHYL-LYSINE (MLYv)
5w: N-DIMETHYL-LYSINE (MLYw)
5x: N-DIMETHYL-LYSINE (MLYx)
5y: N-DIMETHYL-LYSINE (MLYy)
5z: N-DIMETHYL-LYSINE (MLYz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
3
Ligand/Ion
CHLORIDE ION
2
EPC
2
Ligand/Ion
(1S)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]ETHYLPHOSPHONIC ACID
3
IN5
2
Ligand/Ion
{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONICACID
4
MG
3
Ligand/Ion
MAGNESIUM ION
5
MLY
36
Mod. Amino Acid
N-DIMETHYL-LYSINE
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU B:155
BINDING SITE FOR RESIDUE MG B1390
02
AC2
SOFTWARE
MLY A:333 , HOH A:2167 , HOH A:2336
BINDING SITE FOR RESIDUE MG A1390
03
AC3
SOFTWARE
ILE A:263
BINDING SITE FOR RESIDUE MG A1391
04
AC4
SOFTWARE
ASN A:131 , ARG A:138
BINDING SITE FOR RESIDUE CL A1392
05
AC5
SOFTWARE
ASN B:131 , ARG B:138
BINDING SITE FOR RESIDUE CL B1391
06
AC6
SOFTWARE
ARG A:144 , PHE A:215 , GLN A:216 , HOH A:2183 , HOH A:2259
BINDING SITE FOR RESIDUE CL A1393
07
AC7
SOFTWARE
TYR A:270 , THR A:316 , MET A:317 , LYS B:41 , TYR B:45 , ARG B:138 , HIS B:168 , ASN B:208 , SER B:209 , ARG B:224 , GLY B:226 , ILE B:227 , TYR B:359 , HOH B:2443 , HOH B:2444 , HOH B:2445 , HOH B:2446 , HOH B:2447
BINDING SITE FOR RESIDUE IN5 B1392
08
AC8
SOFTWARE
VAL A:39 , LYS A:41 , TYR A:45 , ARG A:138 , HIS A:168 , ASN A:208 , SER A:209 , ARG A:224 , GLY A:226 , ILE A:227 , TYR A:359 , HOH A:2421 , HOH A:2422 , HOH A:2423 , HOH A:2424 , TYR B:270 , TYR B:289 , THR B:316 , MET B:317 , ASP B:318 , HOH B:2318
BINDING SITE FOR RESIDUE IN5 A1394
09
AC9
SOFTWARE
TYR A:270 , TYR A:289 , THR A:316 , MET A:317 , LYS B:41 , TYR B:45 , ARG B:138 , HIS B:168 , ASN B:208 , SER B:209 , ARG B:224 , GLY B:226 , ILE B:227 , TYR B:359 , HOH B:2443 , HOH B:2444 , HOH B:2445 , HOH B:2446 , HOH B:2447
BINDING SITE FOR RESIDUE EPC B1393
10
BC1
SOFTWARE
LYS A:41 , TYR A:45 , ARG A:138 , HIS A:168 , ASN A:208 , SER A:209 , ARG A:224 , GLY A:226 , ILE A:227 , TYR A:359 , HOH A:2421 , HOH A:2422 , HOH A:2423 , HOH A:2424 , TYR B:270 , TYR B:289 , THR B:316 , MET B:317 , ASP B:318
BINDING SITE FOR RESIDUE EPC A1395
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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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_2vd9A02 (A:16-229)
1b: CATH_2vd9B02 (B:16-229)
2a: CATH_2vd9A01 (A:4-15,A:249-389)
2b: CATH_2vd9B01 (B:4-15,B:249-389)
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Classes
(
)
(
)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
2vd9A02
A:16-229
1b
2vd9B02
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
2vd9A01
A:4-15,A:249-389
2b
2vd9B01
B:4-15,B:249-389
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Ala_racemase_N_2vd9B01 (B:14-234)
1b: PFAM_Ala_racemase_N_2vd9B02 (B:14-234)
2a: PFAM_Ala_racemase_C_2vd9B03 (B:249-374)
2b: PFAM_Ala_racemase_C_2vd9B04 (B:249-374)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
Ala_racemase_N
(19)
Bacillus anthracis
(2)
1a
Ala_racemase_N-2vd9B01
B:14-234
1b
Ala_racemase_N-2vd9B02
B:14-234
Clan
:
no clan defined [family: Ala_racemase_C]
(18)
Family
:
Ala_racemase_C
(18)
Bacillus anthracis
(2)
2a
Ala_racemase_C-2vd9B03
B:249-374
2b
Ala_racemase_C-2vd9B04
B:249-374
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
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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set label size to 20 (allowed range: 1-58)
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