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2YZN
Biol. Unit 1
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Asym.Unit (154 KB)
Biol.Unit 1 (101 KB)
Biol.Unit 2 (99 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D-ALANINE:D-ALANINE LIGASE WITH AMPPNP FROM THERMUS THERMOPHILUS HB8.
Authors
:
Y. Kitamuta, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
06 May 07 (Deposition) - 06 Nov 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C (2x)
Keywords
:
D-Alanine:D-Alanine Ligase, Cell Shape, Peptidoglycan Synthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase
(Keyword Search:
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Reference
:
Y. Kitamura, S. Yokoyama, S. Kuramitsu
Crystal Structure Of D-Alanine:D-Alanine Ligase With Amppnp From Thermus Thermophilus Hb8
To Be Published
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
1c: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPc)
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No.
Name
Count
Type
Full Name
1
ANP
2
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
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Sites
(3, 3)
Info
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1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:116 , PHE A:151 , LYS A:153 , SER A:160 , ILE A:163 , GLU A:189 , LYS A:190 , LEU A:192 , GLU A:197 , ASN A:281 , GLU A:282
BINDING SITE FOR RESIDUE ANP A 401
2
AC2
SOFTWARE
LYS B:116 , VAL B:131 , PHE B:151 , LYS B:153 , THR B:157 , GLY B:158 , SER B:159 , 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 , ALA C:220
BINDING SITE FOR RESIDUE ANP B 402
3
AC3
SOFTWARE
ALA B:220 , LYS C:116 , PHE C:151 , LYS C:153 , SER C:159 , SER C:160 , LYS C:190 , ALA C:191 , LEU C:192 , GLU C:197 , ARG C:268 , PHE C:272 , ASN C:281 , GLU C:282 , ASN C:284
BINDING SITE FOR RESIDUE ANP C 403
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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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: DALA_DALA_LIGASE_1 (A:82-93,B:82-93)
2: DALA_DALA_LIGASE_2 (A:261-288,B:261-288)
;
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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
2
A:82-93
B:82-93
-
2
DALA_DALA_LIGASE_2
PS00844
D-alanine--D-alanine ligase signature 2.
DDL_THET8
261-288
2
A:261-288
B:261-288
-
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2yzna2 (A:115-319)
1b: SCOP_d2yznb2 (B:115-319)
1c: SCOP_d2yznc2 (C:115-319)
2a: SCOP_d2yzna1 (A:1-114)
2b: SCOP_d2yznb1 (B:1-114)
2c: SCOP_d2yznc1 (C:1-114)
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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
d2yzna2
A:115-319
1b
d2yznb2
B:115-319
1c
d2yznc2
C: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 HB8 [TaxId: 300852]
(3)
2a
d2yzna1
A:1-114
2b
d2yznb1
B:1-114
2c
d2yznc1
C:1-114
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CATH Domains
(0, 0)
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Dala_Dala_lig_C_2yznC01 (C:122-315)
1b: PFAM_Dala_Dala_lig_C_2yznC02 (C:122-315)
1c: PFAM_Dala_Dala_lig_C_2yznC03 (C:122-315)
2a: PFAM_Dala_Dala_lig_N_2yznC04 (C:1-105)
2b: PFAM_Dala_Dala_lig_N_2yznC05 (C:1-105)
2c: PFAM_Dala_Dala_lig_N_2yznC06 (C: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-2yznC01
C:122-315
1b
Dala_Dala_lig_C-2yznC02
C:122-315
1c
Dala_Dala_lig_C-2yznC03
C: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-2yznC04
C:1-105
2b
Dala_Dala_lig_N-2yznC05
C:1-105
2c
Dala_Dala_lig_N-2yznC06
C:1-105
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