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Asym. Unit
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Asym.Unit (436 KB)
Biol.Unit 1 (215 KB)
Biol.Unit 2 (215 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D-ALANINE--D-ALANINE LIGASE FROM BACILLUS ANTHRACIS COMPLEXED WITH ATP
Authors
:
Y. Kim, R. Mulligan, J. Hasseman, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date
:
20 Mar 11 (Deposition) - 06 Apr 11 (Release) - 01 Jul 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Alpha-Beta Structure, Ligase, Cytosol, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kim, J. Hasseman, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed With Atp
To Be Published
[
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Hetero Components
(6, 70)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
2a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
2d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
3g: CALCIUM ION (CAg)
4a: 1,2-ETHANEDIOL (EDOa)
5a: MAGNESIUM ION (MGa)
6a: SELENOMETHIONINE (MSEa)
6aa: SELENOMETHIONINE (MSEaa)
6ab: SELENOMETHIONINE (MSEab)
6ac: SELENOMETHIONINE (MSEac)
6ad: SELENOMETHIONINE (MSEad)
6ae: SELENOMETHIONINE (MSEae)
6af: SELENOMETHIONINE (MSEaf)
6ag: SELENOMETHIONINE (MSEag)
6ah: SELENOMETHIONINE (MSEah)
6ai: SELENOMETHIONINE (MSEai)
6aj: SELENOMETHIONINE (MSEaj)
6ak: SELENOMETHIONINE (MSEak)
6al: SELENOMETHIONINE (MSEal)
6am: SELENOMETHIONINE (MSEam)
6an: SELENOMETHIONINE (MSEan)
6ao: SELENOMETHIONINE (MSEao)
6ap: SELENOMETHIONINE (MSEap)
6aq: SELENOMETHIONINE (MSEaq)
6ar: SELENOMETHIONINE (MSEar)
6as: SELENOMETHIONINE (MSEas)
6at: SELENOMETHIONINE (MSEat)
6au: SELENOMETHIONINE (MSEau)
6av: SELENOMETHIONINE (MSEav)
6aw: SELENOMETHIONINE (MSEaw)
6ax: SELENOMETHIONINE (MSEax)
6ay: SELENOMETHIONINE (MSEay)
6az: SELENOMETHIONINE (MSEaz)
6b: SELENOMETHIONINE (MSEb)
6ba: SELENOMETHIONINE (MSEba)
6bb: SELENOMETHIONINE (MSEbb)
6bc: SELENOMETHIONINE (MSEbc)
6bd: SELENOMETHIONINE (MSEbd)
6c: SELENOMETHIONINE (MSEc)
6d: SELENOMETHIONINE (MSEd)
6e: SELENOMETHIONINE (MSEe)
6f: SELENOMETHIONINE (MSEf)
6g: SELENOMETHIONINE (MSEg)
6h: SELENOMETHIONINE (MSEh)
6i: SELENOMETHIONINE (MSEi)
6j: SELENOMETHIONINE (MSEj)
6k: SELENOMETHIONINE (MSEk)
6l: SELENOMETHIONINE (MSEl)
6m: SELENOMETHIONINE (MSEm)
6n: SELENOMETHIONINE (MSEn)
6o: SELENOMETHIONINE (MSEo)
6p: SELENOMETHIONINE (MSEp)
6q: SELENOMETHIONINE (MSEq)
6r: SELENOMETHIONINE (MSEr)
6s: SELENOMETHIONINE (MSEs)
6t: SELENOMETHIONINE (MSEt)
6u: SELENOMETHIONINE (MSEu)
6v: SELENOMETHIONINE (MSEv)
6w: SELENOMETHIONINE (MSEw)
6x: SELENOMETHIONINE (MSEx)
6y: SELENOMETHIONINE (MSEy)
6z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
1
Ligand/Ion
ACETIC ACID
2
ATP
4
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
3
CA
7
Ligand/Ion
CALCIUM ION
4
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
5
MG
1
Ligand/Ion
MAGNESIUM ION
6
MSE
56
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(14, 14)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:248 , GLU A:260 , ATP A:402 , HOH A:706
BINDING SITE FOR RESIDUE CA A 401
02
AC2
SOFTWARE
LYS A:95 , VAL A:134 , LYS A:136 , VAL A:146 , GLU A:172 , LYS A:173 , TYR A:174 , ILE A:175 , GLU A:179 , MSE A:259 , GLU A:260 , ASN A:262 , CA A:401 , HOH A:573 , HOH A:598 , HOH A:687 , HOH A:688 , HOH A:706
BINDING SITE FOR RESIDUE ATP A 402
03
AC3
SOFTWARE
ASP B:248 , GLU B:260 , ATP B:402
BINDING SITE FOR RESIDUE CA B 401
04
AC4
SOFTWARE
GLU B:66 , LYS B:95 , VAL B:134 , LYS B:136 , GLY B:145 , VAL B:146 , GLU B:172 , LYS B:173 , TYR B:174 , ILE B:175 , GLU B:179 , MSE B:250 , MSE B:259 , GLU B:260 , ASN B:262 , CA B:401 , HOH B:651
BINDING SITE FOR RESIDUE ATP B 402
05
AC5
SOFTWARE
ASN A:31 , HOH A:681 , GLY B:281 , HOH B:619 , HOH B:620 , HOH B:621 , HOH B:622
BINDING SITE FOR RESIDUE CA B 403
06
AC6
SOFTWARE
ARG C:246 , ASP C:248 , GLU C:260 , ATP C:402 , HOH C:616
BINDING SITE FOR RESIDUE CA C 401
07
AC7
SOFTWARE
LYS C:63 , LYS C:95 , VAL C:134 , LYS C:136 , VAL C:146 , GLU C:172 , LYS C:173 , TYR C:174 , ILE C:175 , GLU C:179 , MSE C:250 , MSE C:259 , GLU C:260 , CA C:401 , HOH C:616 , HOH C:618
BINDING SITE FOR RESIDUE ATP C 402
08
AC8
SOFTWARE
PHE A:131 , HOH A:629 , HOH A:686 , GLU C:108 , HOH C:637
BINDING SITE FOR RESIDUE CA C 403
09
AC9
SOFTWARE
ARG C:299 , GLU C:302 , HOH C:643 , HOH C:644 , HOH C:645
BINDING SITE FOR RESIDUE MG C 404
10
BC1
SOFTWARE
ASP A:203 , HOH A:525 , ASP D:248 , GLU D:260 , ATP D:402 , HOH D:660
BINDING SITE FOR RESIDUE CA D 401
11
BC2
SOFTWARE
PHE A:201 , ASP A:203 , HOH A:525 , HOH A:569 , HOH A:661 , LYS D:95 , VAL D:134 , LYS D:136 , VAL D:146 , GLU D:172 , LYS D:173 , TYR D:174 , ILE D:175 , GLU D:179 , MSE D:250 , MSE D:259 , GLU D:260 , ASN D:262 , CA D:401 , HOH D:527 , HOH D:615 , HOH D:625 , HOH D:660 , HOH D:677 , HOH D:691 , HOH D:700
BINDING SITE FOR RESIDUE ATP D 402
12
BC3
SOFTWARE
ASP A:253 , GLU D:200 , ASP D:203 , TYR D:208 , HOH D:667 , HOH D:668
BINDING SITE FOR RESIDUE CA D 403
13
BC4
SOFTWARE
GLU D:75 , ARG D:299 , GLU D:302 , PHE D:304 , HOH D:726
BINDING SITE FOR RESIDUE EDO D 404
14
BC5
SOFTWARE
ASP D:111 , HOH D:623
BINDING SITE FOR RESIDUE ACY D 405
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: DALA_DALA_LIGASE_1 (A:61-72,B:61-72,C:61-72,D:61-72)
2: DALA_DALA_LIGASE_2 (A:239-266,B:239-266,C:239-266,D:23...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DALA_DALA_LIGASE_1
PS00843
D-alanine--D-alanine ligase signature 1.
DDL_BACAN
61-72
4
A:61-72
B:61-72
C:61-72
D:61-72
2
DALA_DALA_LIGASE_2
PS00844
D-alanine--D-alanine ligase signature 2.
DDL_BACAN
239-266
4
A:239-266
B:239-266
C:239-266
D:239-266
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3r5xa1 (A:94-303)
1b: SCOP_d3r5xb1 (B:94-303)
1c: SCOP_d3r5xc1 (C:94-304)
1d: SCOP_d3r5xd1 (D:94-304)
2a: SCOP_d3r5xa2 (A:-2-93)
2b: SCOP_d3r5xb2 (B:0-93)
2c: SCOP_d3r5xc2 (C:0-93)
2d: SCOP_d3r5xd2 (D:-1-93)
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Classes
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Folds
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Superfamilies
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(
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Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
automated matches
(42)
Protein domain
:
automated matches
(42)
Anthrax bacillus (Bacillus anthracis) [TaxId: 1392]
(1)
1a
d3r5xa1
A:94-303
1b
d3r5xb1
B:94-303
1c
d3r5xc1
C:94-304
1d
d3r5xd1
D:94-304
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
D-Alanine ligase N-terminal domain
(7)
Protein domain
:
D-Ala-D-Ala ligase, N-domain
(5)
Anthrax bacillus (Bacillus anthracis) [TaxId: 1392]
(1)
2a
d3r5xa2
A:-2-93
2b
d3r5xb2
B:0-93
2c
d3r5xc2
C:0-93
2d
d3r5xd2
D:-1-93
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Dala_Dala_lig_C_3r5xD01 (D:101-293)
1b: PFAM_Dala_Dala_lig_C_3r5xD02 (D:101-293)
1c: PFAM_Dala_Dala_lig_C_3r5xD03 (D:101-293)
1d: PFAM_Dala_Dala_lig_C_3r5xD04 (D:101-293)
2a: PFAM_Dala_Dala_lig_N_3r5xD05 (D:41-84)
2b: PFAM_Dala_Dala_lig_N_3r5xD06 (D:41-84)
2c: PFAM_Dala_Dala_lig_N_3r5xD07 (D:41-84)
2d: PFAM_Dala_Dala_lig_N_3r5xD08 (D:41-84)
2e: PFAM_Dala_Dala_lig_N_3r5xD09 (D:41-84)
2f: PFAM_Dala_Dala_lig_N_3r5xD10 (D:41-84)
2g: PFAM_Dala_Dala_lig_N_3r5xD11 (D:41-84)
2h: PFAM_Dala_Dala_lig_N_3r5xD12 (D:41-84)
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Clans
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(
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Families
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(
)
Organisms
(
)
(
)
Clan
:
ATP-grasp
(83)
Family
:
Dala_Dala_lig_C
(12)
Bacillus anthracis
(2)
1a
Dala_Dala_lig_C-3r5xD01
D:101-293
1b
Dala_Dala_lig_C-3r5xD02
D:101-293
1c
Dala_Dala_lig_C-3r5xD03
D:101-293
1d
Dala_Dala_lig_C-3r5xD04
D:101-293
Clan
:
no clan defined [family: Dala_Dala_lig_N]
(12)
Family
:
Dala_Dala_lig_N
(12)
Bacillus anthracis
(2)
2a
Dala_Dala_lig_N-3r5xD05
D:41-84
2b
Dala_Dala_lig_N-3r5xD06
D:41-84
2c
Dala_Dala_lig_N-3r5xD07
D:41-84
2d
Dala_Dala_lig_N-3r5xD08
D:41-84
2e
Dala_Dala_lig_N-3r5xD09
D:41-84
2f
Dala_Dala_lig_N-3r5xD10
D:41-84
2g
Dala_Dala_lig_N-3r5xD11
D:41-84
2h
Dala_Dala_lig_N-3r5xD12
D:41-84
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Asym.Unit (436 KB)
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