5C1P - JenaLib

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Title :   CRYSTAL STRUCTURE OF ADP AND D-ALANYL-D-ALANINE COMPLEXED D-ALANINE-D-ALANINE LIGASE(DDL) FROM YERSINIA PESTIS

Authors :   H. T. Tran, L. W. Kang, M. K. Hong, H. P. T. Ngo

Date :   15 Jun 15 (Deposition) - 02 Mar 16 (Release) - 02 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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, Ddl, Drug Target, Bacterial Cell Wall Synthesis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. T. Tran, M. K. Hong, H. P. Ngo, K. H. Huynh, Y. J. Ahn, Z. Wang, L. W. Kang
Structure Of D-Alanine-D-Alanine Ligase From Yersinia Pestis: Nucleotide Phosphate Recognition By The Serine Loop
Acta Crystallogr D Struct V. 72 12 2016 Biol
PubMed-ID: 26894530 | Reference-DOI: 10.1107/S2059798315021671

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21-GOLD(DE3)PLYSS AG
	Expression System Strain	:	BL21-GOLD(DE3)PLYSS AG
	Expression System Taxid	:	866768
	Gene	:	DDL, DDLB, YPO0557, Y3624, YP_3627
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Synonym	:	D-ALA-D-ALA LIGASE,D-ALANYLALANINE SYNTHETASE

		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 (5, 18)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	DAL	2	Ligand/Ion	D-ALANINE
4	GOL	7	Ligand/Ion	GLYCEROL
5	NA	5	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	DAL	-1	Ligand/Ion	D-ALANINE
4	GOL	3	Ligand/Ion	GLYCEROL
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (4, 9)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	DAL	2	Ligand/Ion	D-ALANINE
4	GOL	4	Ligand/Ion	GLYCEROL
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:68 , SER A:91 , THR A:94 , MET A:95 , THR A:273 , HOH A:517	binding site for residue NA A 401
02	AC2	SOFTWARE	GLY A:11 , THR A:12 , THR A:42 , GLY A:66	binding site for residue GOL A 402
03	AC3	SOFTWARE	GLU A:77 , GLN A:80 , LEU A:81 , TYR A:83 , ASP A:306	binding site for residue GOL A 403
04	AC4	SOFTWARE	LYS B:97 , ILE B:142 , LYS B:144 , GLU B:180 , LYS B:181 , LEU B:183 , GLU B:187 , TYR B:210 , MET B:259 , GLU B:270	binding site for residue ADP B 401
05	AC5	SOFTWARE	GLU B:68 , SER B:91 , THR B:94 , MET B:95 , THR B:273 , HOH B:512	binding site for residue NA B 402
06	AC6	SOFTWARE	GLY B:11 , THR B:12 , THR B:42 , GLY B:66	binding site for residue GOL B 403
07	AC7	SOFTWARE	LYS C:97 , ILE C:142 , LYS C:144 , GLU C:148 , SER C:151 , MET C:154 , GLU C:180 , LYS C:181 , LEU C:183 , GLU C:187 , PHE C:209 , TYR C:210 , LYS C:215 , MET C:259 , GLU C:270	binding site for residue ADP C 401
08	AC8	SOFTWARE	GLU C:68 , SER C:91 , THR C:94 , MET C:95 , THR C:273 , HOH C:543	binding site for residue NA C 402
09	AC9	SOFTWARE	ARG C:255 , GLY C:276 , SER C:281 , LEU C:282 , HOH C:501 , HOH C:519 , HOH C:533	binding site for residue ACT C 403
10	AD1	SOFTWARE	ALA C:247	binding site for residue GOL C 404
11	AD2	SOFTWARE	ASP A:306 , GLN C:296 , ARG C:300 , HOH C:547	binding site for residue GOL C 405
12	AD3	SOFTWARE	LEU C:76 , GLU C:77 , LEU C:81 , ASP C:306 , GOL C:407	binding site for residue GOL C 406
13	AD4	SOFTWARE	PRO C:82 , TYR C:83 , GLY C:85 , GLY C:87 , ASP C:306 , GOL C:406	binding site for residue GOL C 407
14	AD5	SOFTWARE	HIS A:265 , HOH A:507 , HIS C:280 , HOH C:575	binding site for residue NA C 408
15	AD6	SOFTWARE	LYS D:97 , ILE D:142 , LYS D:144 , GLU D:148 , GLU D:180 , LYS D:181 , TRP D:182 , LEU D:183 , GLU D:187 , PHE D:209 , TYR D:210 , MET D:259 , GLU D:270 , HOH D:527	binding site for residue ADP D 401
16	AD7	SOFTWARE	GLU D:68 , SER D:91 , THR D:94 , MET D:95 , THR D:273 , HOH D:508	binding site for residue NA D 404
17	AD8	SOFTWARE	TYR D:210 , LYS D:215 , TYR D:216 , ARG D:255 , ASN D:272 , PRO D:275 , GLY D:276 , SER D:281 , LEU D:282 , HOH D:505 , HOH D:506	binding site for Di-peptide DAL D 402 and DAL D 403

(no "SS Bond" information available for 5C1P)

Asymmetric Unit

No.	Residues
1	Leu A:139	-	Pro A:140
2	Gly A:185	-	Pro A:186
3	Cys A:225	-	Pro A:226
4	Leu B:139	-	Pro B:140
5	Gly B:185	-	Pro B:186
6	Cys B:225	-	Pro B:226
7	Leu C:139	-	Pro C:140
8	Gly C:185	-	Pro C:186
9	Cys C:225	-	Pro C:226
10	Leu D:139	-	Pro D:140
11	Gly D:185	-	Pro D:186
12	Cys D:225	-	Pro D:226

(no "SAP(SNP)/Variant" information available for 5C1P)

(no "PROSITE Motif" information available for 5C1P)

(no "Exon" information available for 5C1P)

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
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Chain A from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhh..eeeee......eee.hhhhhhhhhhhhhh...eeeeee.....eeeeeee..ee...eeee...eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1p A   1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHSVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |153       163       173       183       193       203 ||    227       237       247       257       267       277       287       297         
                                                                                                                                                                            147|                                                   205|                                                                                      
                                                                                                                                                                             151                                                    220

Chain B from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhh......eeeeehhhhhh...hhhhhhhhhhh..eeeee.....eee.hhhhhhhhhhhhh....eeeeee.....eeeeeee..ee...eeee.............eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1p B   1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFYDYDAKKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |154       164       174       184       194       204       214||     228       238       248       258       268       278       288       298        
                                                                                                                                                                            147|                                                            215|                                                                                      
                                                                                                                                                                             152                                                             220

Chain C from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhh...eeeeee.....eeeeeee..ee...eeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c1p C   1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGSSVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    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

Chain D from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhh..eeeee......eee.hhhhhhhhhhhhh....eeeeee.....eeeeeee..ee...eeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1p D   2 AEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      |154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304  
                                                                                                                                                                            148|                                                                                                                                                          
                                                                                                                                                                             152

Legend:		→ Mismatch	(orange background)
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	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 '\|'

(no "SCOP Domain" information available for 5C1P)

(no "CATH Domain" information available for 5C1P)

(no "Pfam Domain" information available for 5C1P)

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	Cis Peptide Bonds
		Cys A:225 - Pro A:226	[ RasMol ]
		Cys B:225 - Pro B:226	[ RasMol ]
		Cys C:225 - Pro C:226	[ RasMol ]
		Cys D:225 - Pro D:226	[ RasMol ]
		Gly A:185 - Pro A:186	[ RasMol ]
		Gly B:185 - Pro B:186	[ RasMol ]
		Gly C:185 - Pro C:186	[ RasMol ]
		Gly D:185 - Pro D:186	[ RasMol ]
		Leu A:139 - Pro A:140	[ RasMol ]
		Leu B:139 - Pro B:140	[ RasMol ]
		Leu C:139 - Pro C:140	[ RasMol ]
		Leu D:139 - Pro D:140	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (5, 18)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

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