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2ZDG
Asym. Unit
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Asym.Unit (204 KB)
Biol.Unit 1 (99 KB)
Biol.Unit 2 (104 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D-ALANINE:D-ALANINE LIGASE WITH ADP FROM THERMUS THERMOPHIUS HB8
Authors
:
Y. Kitamura, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
22 Nov 07 (Deposition) - 27 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
D-Alanine-D-Alanine Ligase, Peptidoglycan Biosynthesis, Cell Shape, Cell Wall Biogenesis/Degradation, Peptidoglycan Synthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
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Reference
:
Y. Kitamura, S. Yokoyama, S. Kuramitsu
Crystal Structure Of D-Alanine:D-Alanine Ligase With Adp From Thermus Thermophius Hb8
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP C:270 , GLU C:282
BINDING SITE FOR RESIDUE MG C 601
2
AC2
SOFTWARE
ASP D:270 , GLU D:282
BINDING SITE FOR RESIDUE MG D 602
3
AC3
SOFTWARE
LYS A:116 , PHE A:151 , LYS A:153 , GLY A:158 , SER A:159 , SER A:160 , ILE A:163 , GLU A:189 , LYS A:190 , ALA A:191 , LEU A:192 , GLU A:197 , PHE A:272 , ASN A:281 , GLU A:282
BINDING SITE FOR RESIDUE ADP A 401
4
AC4
SOFTWARE
LYS B:116 , PHE B:151 , LYS B:153 , SER B:160 , ILE B:163 , GLU B:189 , LYS B:190 , ALA B:191 , LEU B:192 , GLU B:197 , PHE B:272 , ASN B:281 , GLU B:282
BINDING SITE FOR RESIDUE ADP B 402
5
AC5
SOFTWARE
LYS C:116 , PHE C:151 , LYS C:153 , GLY C:158 , SER C:159 , SER C:160 , ILE C:163 , GLU C:189 , LYS C:190 , ALA C:191 , LEU C:192 , GLU C:197 , TYR C:218 , PHE C:222 , TYR C:223 , LYS C:228 , PHE C:272 , ASN C:281 , GLU C:282
BINDING SITE FOR RESIDUE ADP C 403
6
AC6
SOFTWARE
ALA B:220 , LYS D:116 , PHE D:151 , LYS D:153 , SER D:159 , SER D:160 , ILE D:163 , GLU D:189 , LYS D:190 , LEU D:192 , GLU D:197 , PHE D:272 , ASN D:281 , GLU D:282
BINDING SITE FOR RESIDUE ADP D 404
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: DALA_DALA_LIGASE_1 (A:82-93,B:82-93,C:82-93,D:82-93)
2: DALA_DALA_LIGASE_2 (A:261-288,B:261-288,C:261-288,D:26...)
;
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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_THET8
82-93
4
A:82-93
B:82-93
C:82-93
D:82-93
2
DALA_DALA_LIGASE_2
PS00844
D-alanine--D-alanine ligase signature 2.
DDL_THET8
261-288
4
A:261-288
B:261-288
C:261-288
D:261-288
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2zdga2 (A:115-319)
1b: SCOP_d2zdgb2 (B:115-319)
1c: SCOP_d2zdgc2 (C:115-319)
1d: SCOP_d2zdgd2 (D:115-319)
2a: SCOP_d2zdga1 (A:1-114)
2b: SCOP_d2zdgb1 (B:1-114)
2c: SCOP_d2zdgc1 (C:1-114)
2d: SCOP_d2zdgd1 (D:1-114)
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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)
Thermus thermophilus HB8 [TaxId: 300852]
(6)
1a
d2zdga2
A:115-319
1b
d2zdgb2
B:115-319
1c
d2zdgc2
C:115-319
1d
d2zdgd2
D:115-319
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
automated matches
(45)
Protein domain
:
automated matches
(45)
Thermus thermophilus [TaxId: 274]
(4)
2a
d2zdga1
A:1-114
2b
d2zdgb1
B:1-114
2c
d2zdgc1
C:1-114
2d
d2zdgd1
D:1-114
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CATH Domains
(0, 0)
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Dala_Dala_lig_C_2zdgD01 (D:122-315)
1b: PFAM_Dala_Dala_lig_C_2zdgD02 (D:122-315)
1c: PFAM_Dala_Dala_lig_C_2zdgD03 (D:122-315)
1d: PFAM_Dala_Dala_lig_C_2zdgD04 (D:122-315)
2a: PFAM_Dala_Dala_lig_N_2zdgD05 (D:1-105)
2b: PFAM_Dala_Dala_lig_N_2zdgD06 (D:1-105)
2c: PFAM_Dala_Dala_lig_N_2zdgD07 (D:1-105)
2d: PFAM_Dala_Dala_lig_N_2zdgD08 (D:1-105)
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Clan
:
ATP-grasp
(83)
Family
:
Dala_Dala_lig_C
(12)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(6)
1a
Dala_Dala_lig_C-2zdgD01
D:122-315
1b
Dala_Dala_lig_C-2zdgD02
D:122-315
1c
Dala_Dala_lig_C-2zdgD03
D:122-315
1d
Dala_Dala_lig_C-2zdgD04
D:122-315
Clan
:
no clan defined [family: Dala_Dala_lig_N]
(12)
Family
:
Dala_Dala_lig_N
(12)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(6)
2a
Dala_Dala_lig_N-2zdgD05
D:1-105
2b
Dala_Dala_lig_N-2zdgD06
D:1-105
2c
Dala_Dala_lig_N-2zdgD07
D:1-105
2d
Dala_Dala_lig_N-2zdgD08
D:1-105
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