4QDI - JenaLib

Title :   CRYSTAL STRUCTURE II OF MURF FROM ACINETOBACTER BAUMANNII

Authors :   Y. J. An, C. S. Jeong, S. S. Cha

Date :   13 May 14 (Deposition) - 01 Apr 15 (Release) - 01 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Udp-N-Acetylmuramoyl-Tripeptide-D-Alanyl-D-Ananine Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. S. Cha, Y. J. An, C. S. Jeong, J. H. Yu, K. M. Chung
Atp-Binding Mode Including A Carbamoylated Lysine And Two Mg(2+) Ions, And Substrate-Binding Mode In Acinetobacter Baumannii Murf
Biochem. Biophys. Res. Commun. V. 450 1045 2014
PubMed-ID: 24978312 | Reference-DOI: 10.1016/J.BBRC.2014.06.108

Compounds

Molecule 1 - UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
	Chains	:	A
	EC Number	:	6.3.2.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET-A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ABBFA_000315
	Organism Scientific	:	ACINETOBACTER BAUMANNII
	Organism Taxid	:	557600
	Strain	:	AB307-0294

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:122 , SER A:123 , GLY A:124 , LYS A:125 , THR A:126 , THR A:127 , ASN A:197 , HIS A:292 , ASN A:296 , ARG A:327 , TYR A:343 , ASN A:344 , SER A:349 , MG A:503 , HOH A:664 , HOH A:692 , HOH A:735 , HOH A:776 , HOH A:782 , HOH A:791 , HOH A:853	BINDING SITE FOR RESIDUE ATP A 501
2	AC2	SOFTWARE	THR A:42 , PHE A:61 , ARG A:97 , LEU A:153 , GLN A:226 , GLN A:249 , HOH A:611 , HOH A:769 , HOH A:792 , HOH A:835 , HOH A:836 , HOH A:855	BINDING SITE FOR RESIDUE UDP A 502
3	AC3	SOFTWARE	THR A:126 , GLU A:172 , ATP A:501 , HOH A:794	BINDING SITE FOR RESIDUE MG A 503
4	AC4	SOFTWARE	ASP A:152 , TYR A:183 , PHE A:283 , HOH A:646 , HOH A:736 , HOH A:737 , HOH A:842	BINDING SITE FOR RESIDUE EDO A 504
5	AC5	SOFTWARE	PRO A:13 , TRP A:14 , GLN A:18 , ARG A:107 , HOH A:663 , HOH A:854	BINDING SITE FOR RESIDUE EDO A 505

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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)
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Chain A from PDB  Type:PROTEIN  Length:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh.ee.hhh.......eee.........eeee..ee..ee...hhhhhhhh...eeee........eeee..hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.eee........hhhhhhhh.......eeeee......hhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhh......eeeee....hhhhhhhhh...eeeee......eeeeeee....eeeeeee..eeeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh........eeeee..eeeee.....hhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhh......eeee..hhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdi A   9 VPLEPWTAQQLQQATQGYWHKDQIPQTEIKRILTDSRHAESGDAFLALKGERFDAHNFVAQVVANGCQVAIVERPIDAEIAQLVVADTRLALGQLGAYRREQNAQLKVIALTGSSGKTTTKEMLGSILSRLAPTLITRGNLNNDLGVPMMLLELRKEHQYAVMELGANHQGEIDYTSKIVQPHVAGILNIGTAHLGEFGGRDGICRAKSEIYRHILPQGVAIVPQQDDFTAEIREAAKSHQIMSFGEGGDVFATEIELLPQSANFQLHTPQGSSFVRLPFAGEHNVQNATAAVAFALALGVSLEDIVKGLEQAQGAKGRLNFIQKAPHLFIDDTYNANPTSMRAAAQVLLQQNGIKVMVMGDIGELGDSSWQEHHDLGRDLAELPLDHIVAVGQFASAALEGAGLHSTKLKAFQTQAEALPFLINLIQTHQPQSMSFLFKGSRFTHMETLMADLMEK 465
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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	Cis Peptide Bonds
		Val A:9 - Pro A:10	[ RasMol ]

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Description