5DG3 - JenaLib

Title :   STRUCTURE OF PSEUDOMONAS AERUGINOSA LPXA IN COMPLEX WITH UDP-3-O-(R-3-HYDROXYDECANOYL)-GLCNAC

Authors :   E. W. Smith, Y. Chen

Date :   27 Aug 15 (Deposition) - 16 Sep 15 (Release) - 14 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D (1x),E (1x),F (1x)

Keywords :   Acyltransferases, Catalytic Domain, Udp-Glcnac, Fatty Acids, Lipid A, Substrate Specificity, Uridine Diphosphate N-Acetylglucosamine, Hydrocarbon Rulers, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. W. Smith, X. Zhang, C. Behzadi, L. D. Andrews, F. Cohen, Y. Chen
Structures Of Pseudomonas Aeruginosa Lpxa Reveal The Basis For Its Substrate Selectivity.
Biochemistry V. 54 5937 2015
PubMed-ID: 26352800 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B00720

Compounds

Molecule 1 - ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O- ACYLTRANSFERASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	2.3.1.129
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	LPXA, PSPA7_1495
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA (STRAIN PA7)
	Organism Taxid	:	381754
	Strain	:	PA7
	Synonym	:	UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE

Structural Features

Chains, Units

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D (1x)	E (1x)	F (1x)

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 5)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	U21	4	Ligand/Ion	URIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYDECANOYL)-N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	-1	Ligand/Ion	PHOSPHATE ION
2	U21	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYDECANOYL)-N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	-1	Ligand/Ion	PHOSPHATE ION
2	U21	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYDECANOYL)-N-ACETYL-D-GLUCOSAMINE

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:114 , VAL A:132 , ASN A:133 , GLY A:151 , PHE A:166 , ASN A:194 , GLU A:196 , GLY A:197 , ARG A:200 , HOH A:309 , ASP B:70 , LEU B:71 , LYS B:72 , HIS B:118 , HIS B:121 , ALA B:136 , ALA B:138 , HIS B:140 , VAL B:155 , HIS B:156 , GLN B:157 , TYR B:158 , HOH B:414 , HOH B:415 , HOH B:428	binding site for residue U21 B 301
2	AC2	SOFTWARE	ASN B:133 , ILE B:148 , PHE B:166 , ASN B:194 , GLU B:196 , ARG B:200 , PRO C:69 , ASP C:70 , LEU C:71 , LYS C:72 , HIS C:118 , HIS C:121 , ALA C:136 , ALA C:138 , HIS C:140 , VAL C:155 , GLN C:157 , HOH C:401	binding site for residue U21 C 301
3	AC3	SOFTWARE	MET D:114 , VAL D:132 , ASN D:133 , ILE D:148 , PHE D:166 , ASN D:194 , GLU D:196 , ARG D:200 , ARG D:201 , HOH D:403 , HOH D:410 , HOH D:411 , HOH D:419 , HOH D:422 , HOH D:433 , ASP F:70 , LEU F:71 , LYS F:72 , HIS F:118 , HIS F:121 , ALA F:136 , ALA F:138 , HIS F:140 , GLN F:157 , HOH F:310	binding site for residue U21 D 301
4	AC4	SOFTWARE	ASP E:70 , LEU E:71 , LYS E:72 , HIS E:118 , HIS E:121 , ALA E:136 , ALA E:138 , HIS E:140 , GLN E:157 , HOH E:405 , MET F:114 , ASN F:133 , ILE F:148 , PHE F:166 , ASN F:194 , GLU F:196 , ARG F:200	binding site for residue U21 E 301
5	AC5	SOFTWARE	ASN E:194 , GLU E:196 , ARG E:200	binding site for residue PO4 E 302

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Asymmetric Unit

No.	Residues
1	Gly A:48	-	Pro A:49
2	Asn A:186	-	Pro A:187
3	Gly B:48	-	Pro B:49
4	Asn B:186	-	Pro B:187
5	Gly C:48	-	Pro C:49
6	Asn C:186	-	Pro C:187
7	Gly D:48	-	Pro D:49
8	Asn D:186	-	Pro D:187
9	Gly E:48	-	Pro E:49
10	Asn E:186	-	Pro E:187
11	Gly F:48	-	Pro F:49
12	Asn F:186	-	Pro F:187

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 A   3 LIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252

Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 B   2 SLIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 C   3 LIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252

Chain D from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee.....eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 D   3 LIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    12        22        32        42        52        62      ||79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249         
                                                                                             69|                                                                                                                                                                                     
                                                                                              77

Chain E from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 E   3 LIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252

Chain F from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 F   2 SLIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

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 (7, 7)

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	Ligands, Modified Residues, Ions
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		U21	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Asn A:186 - Pro A:187	[ RasMol ]
		Asn B:186 - Pro B:187	[ RasMol ]
		Asn C:186 - Pro C:187	[ RasMol ]
		Asn D:186 - Pro D:187	[ RasMol ]
		Asn E:186 - Pro E:187	[ RasMol ]
		Asn F:186 - Pro F:187	[ RasMol ]
		Gly A:48 - Pro A:49	[ RasMol ]
		Gly B:48 - Pro B:49	[ RasMol ]
		Gly C:48 - Pro C:49	[ RasMol ]
		Gly D:48 - Pro D:49	[ RasMol ]
		Gly E:48 - Pro E:49	[ RasMol ]
		Gly F:48 - Pro F:49	[ RasMol ]

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Description