2ZDH - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF D-ALANINE:D-ALANINE LIGASE WITH ADP AND D-ALANINE FROM THERMUS THERMOPHIUS HB8

Authors :   Y. Kitamuta, 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 :   1.90

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: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kitamura, S. Yokoyama, S. Kuramitsu
Crystal Structure Of D-Alanine:D-Alanine Ligase With Adp And D-Alanine From Thermus Thermophius Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Strain	:	HB8

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	DAL	2	Ligand/Ion	D-ALANINE
3	MG	7	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	DAL	1	Ligand/Ion	D-ALANINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	DAL	1	Ligand/Ion	D-ALANINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:282 , ASN A:284	BINDING SITE FOR RESIDUE MG A 811
02	AC2	SOFTWARE	ASP A:270 , GLU A:282	BINDING SITE FOR RESIDUE MG A 812
03	AC3	SOFTWARE	GLU B:282	BINDING SITE FOR RESIDUE MG B 813
04	AC4	SOFTWARE	GLU B:282	BINDING SITE FOR RESIDUE MG B 814
05	AC5	SOFTWARE	GLU C:282	BINDING SITE FOR RESIDUE MG C 815
06	AC6	SOFTWARE	GLU C:282	BINDING SITE FOR RESIDUE MG C 816
07	AC7	SOFTWARE	ASP D:270 , GLU D:282	BINDING SITE FOR RESIDUE MG D 817
08	AC8	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 , TYR A:218 , PHE A:222 , TYR A:223 , LYS A:228 , PHE A:272 , ASN A:281 , GLU A:282	BINDING SITE FOR RESIDUE ADP A 701
09	AC9	SOFTWARE	LYS B:116 , PHE B:151 , LYS B:153 , 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 ADP B 702
10	BC1	SOFTWARE	GLU A:13 , HIS A:82 , TYR A:229 , ARG A:268 , ASN A:284 , GLY A:288	BINDING SITE FOR RESIDUE DAL A 801
11	BC2	SOFTWARE	ALA B:220 , 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 , PHE C:272 , ASN C:281 , GLU C:282	BINDING SITE FOR RESIDUE ADP C 703
12	BC3	SOFTWARE	LYS D:116 , PHE D:151 , LYS D:153 , GLY D:158 , SER D:159 , SER D:160 , ILE D:163 , GLU D:189 , LYS D:190 , LEU D:192 , GLU D:197 , TYR D:218 , PHE D:222 , TYR D:223 , PHE D:272 , ASN D:281 , GLU D:282	BINDING SITE FOR RESIDUE ADP D 704
13	BC4	SOFTWARE	GLU D:13 , HIS D:82 , ARG D:268 , ASN D:284 , GLY D:288	BINDING SITE FOR RESIDUE DAL D 802

(no "SS Bond" information available for 2ZDH)

Asymmetric Unit

No.	Residues
1	Phe A:65	-	Pro A:66
2	Pro A:148	-	Pro A:149
3	Ser A:193	-	Pro A:194
4	Ile A:238	-	Pro A:239
5	Phe B:65	-	Pro B:66
6	Pro B:148	-	Pro B:149
7	Ser B:193	-	Pro B:194
8	Ile B:238	-	Pro B:239
9	Phe C:65	-	Pro C:66
10	Pro C:148	-	Pro C:149
11	Ser C:193	-	Pro C:194
12	Ile C:238	-	Pro C:239
13	Phe D:65	-	Pro D:66
14	Pro D:148	-	Pro D:149
15	Ser D:193	-	Pro D:194
16	Ile D:238	-	Pro D:239

(no "SAP(SNP)/Variant" information available for 2ZDH)

Asymmetric Unit (2, 8)

	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

Biological Unit 1 (2, 4)

	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 - -

Biological Unit 2 (2, 4)

	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	- - C:82-93 D:82-93
2	DALA_DALA_LIGASE_2	PS00844	D-alanine--D-alanine ligase signature 2.	DDL_THET8	261-288	2	- - C:261-288 D:261-288

(no "Exon" information available for 2ZDH)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:319
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2zdha1 A:1-114 automated matches                                                                                 d2zdha2 A:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhhh.............hhhhh.eeee.........hhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhh......eeeee............eeeee.........eee.hhhhhhhhhhhhhh...eeeeee.....eeeeeeee.....eeeeeeeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zdh A   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2zdhb1 B:1-114 automated matches                                                                                 d2zdhb2 B:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhhh.............hhhhh.eeeee........hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhh......eeeee............eeeee.........eee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.....eeeeeeeeee.....-------...eeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zdh B   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFY-------PGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  |      -|      240       250       260       270       280       290       300       310         
                                                                                                                                                                                                                                                        223     231

Chain C from PDB  Type:PROTEIN  Length:316
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2zdhc1 C:1-114 automated matches                                                                                 d2zdhc2 C:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhh..............hhhhh.eeeee........hhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhh......eeeee............eeeee.........eee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.....eeeeeeeeee.....---.......eeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zdh C   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFY---TKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  |   |230       240       250       260       270       280       290       300       310         
                                                                                                                                                                                                                                                        223 227

Chain D from PDB  Type:PROTEIN  Length:319
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2zdhd1 D:1-114 automated matches                                                                                 d2zdhd2 D:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Dala_Dala_lig_N-2zdhD05 D:1-105                                                                          ----------------Dala_Dala_lig_C-2zdhD01 D:122-315                                                                                                                                                                 ---- Pfam domains (1)
           Pfam domains (2) Dala_Dala_lig_N-2zdhD06 D:1-105                                                                          ----------------Dala_Dala_lig_C-2zdhD02 D:122-315                                                                                                                                                                 ---- Pfam domains (2)
           Pfam domains (3) Dala_Dala_lig_N-2zdhD07 D:1-105                                                                          ----------------Dala_Dala_lig_C-2zdhD03 D:122-315                                                                                                                                                                 ---- Pfam domains (3)
           Pfam domains (4) Dala_Dala_lig_N-2zdhD08 D:1-105                                                                          ----------------Dala_Dala_lig_C-2zdhD04 D:122-315                                                                                                                                                                 ---- Pfam domains (4)
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhhh.............hhhhh.eeeee........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeeee............eeeee.........eee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.....eeeeeeeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zdh D   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

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	d2zdha2	A:115-319
1b	d2zdhb2	B:115-319
1c	d2zdhc2	C:115-319
1d	d2zdhd2	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	d2zdha1	A:1-114
2b	d2zdhb1	B:1-114
2c	d2zdhc1	C:1-114
2d	d2zdhd1	D:1-114

(no "CATH Domain" information available for 2ZDH)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DDL_THET8 | Q5SHZ3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008716	D-alanine-D-alanine ligase activity	Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
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		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:238 - Pro A:239	[ RasMol ]
		Ile B:238 - Pro B:239	[ RasMol ]
		Ile C:238 - Pro C:239	[ RasMol ]
		Ile D:238 - Pro D:239	[ RasMol ]
		Phe A:65 - Pro A:66	[ RasMol ]
		Phe B:65 - Pro B:66	[ RasMol ]
		Phe C:65 - Pro C:66	[ RasMol ]
		Phe D:65 - Pro D:66	[ RasMol ]
		Pro A:148 - Pro A:149	[ RasMol ]
		Pro B:148 - Pro B:149	[ RasMol ]
		Pro C:148 - Pro C:149	[ RasMol ]
		Pro D:148 - Pro D:149	[ RasMol ]
		Ser A:193 - Pro A:194	[ RasMol ]
		Ser B:193 - Pro B:194	[ RasMol ]
		Ser C:193 - Pro C:194	[ RasMol ]
		Ser D:193 - Pro D:194	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2zdh
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
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	DDL_THET8 \| Q5SHZ3
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	6.3.2.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
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Access by UniProt ID/Accession number
	DDL_THET8 \| Q5SHZ3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	DDL_THET8 \| Q5SHZ3	:	2fb9 2yzg 2yzm 2yzn 2zdg 2zdq

2yzg	FREE-FORM OF LIGASE
2yzm	COCRYSTAL WITH LIGAND
2zdg	COCRYSTAL WITH ADP RELATED ID: TTK003001114.5 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (16, 16)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (0, 0)

Pfam Domains (2, 8)

Gene Ontology (12, 12)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File