5D6C - JenaLib

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Title :   STRUCTURE OF 4497 FAB BOUND TO SYNTHETIC WALL TEICHOIC ACID FRAGMENT

Authors :   P. J. Lupardus, R. Fong

Date :   12 Aug 15 (Deposition) - 11 Nov 15 (Release) - 02 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym. Unit : A,B,H,L
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: H,L  (1x)

Keywords :   Staphylococcus Aureus Wall Teichoic Acid Antibody Mrsa, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Lehar, T. Pillow, M. Xu, L. Staben, K. K. Kajihara, R. Vandlen, L. Depalatis, H. Raab, W. L. Hazenbos, J. H. Morisaki, J. Kim, S. Park, M. Darwish, B. C. Lee, H. Hernandez, K. M. Loyet, P. Lupardus, R. Fong, D. Yan, C. Chalouni, E. Luis, Y. Khalfin, E. Plise, J. Cheong, J. P. Lyssikatos, M. Strandh, K. Koefoed, P. S. Andersen, J. A. Flygare M. Wah Tan, E. J. Brown, S. Mariathasan
Novel Antibody-Antibiotic Conjugate Eliminates Intracellula S. Aureus.
Nature V. 527 323 2015
PubMed-ID: 26536114 | Reference-DOI: 10.1038/NATURE16057

Molecule 1 - 4497 ANTIBODY IGK (VL AND CL)
	Chains	:	A, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - 4497 ANTIBODY IGG1 (VH AND CH1)
	Chains	:	B, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	57S	2	Ligand/Ion	4-O-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-5-O-PHOSPHONO-D-RIBITOL
2	ACT	2	Ligand/Ion	ACETATE ION
3	CA	4	Ligand/Ion	CALCIUM ION
4	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	57S	1	Ligand/Ion	4-O-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-5-O-PHOSPHONO-D-RIBITOL
2	ACT	-1	Ligand/Ion	ACETATE ION
3	CA	-1	Ligand/Ion	CALCIUM ION
4	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	57S	1	Ligand/Ion	4-O-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-5-O-PHOSPHONO-D-RIBITOL
2	ACT	2	Ligand/Ion	ACETATE ION
3	CA	-1	Ligand/Ion	CALCIUM ION
4	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:97 , PHE A:98 , TRP B:47 , HOH B:489	binding site for residue CA A 301
2	AC2	SOFTWARE	ALA A:12 , PRO L:65 , ARG L:67	binding site for residue CA A 302
3	AC3	SOFTWARE	ARG A:27D , ARG A:28 , LEU A:32 , TYR A:91 , SER B:31 , PHE B:32 , TRP B:33 , ASN B:52A , GLY B:95 , ASP B:96 , HOH B:407 , HOH B:451 , 57S L:303	binding site for residue 57S B 301
4	AC4	SOFTWARE	TRP H:47 , THR L:103 , PHE L:104	binding site for residue CA H 301
5	AC5	SOFTWARE	GLY H:189 , THR H:190 , THR H:192 , LYS H:209	binding site for residue ACT H 302
6	AC6	SOFTWARE	PRO H:122 , LYS H:208 , LYS H:209 , VAL H:210 , GLU H:211 , HOH H:416 , GLU L:129 , HOH L:414	binding site for residue GOL H 303
7	AC7	SOFTWARE	GLN L:153 , TRP L:154 , GLN L:161	binding site for residue CA L 301
8	AC8	SOFTWARE	HIS H:163 , GLU L:171 , ASP L:173 , HOH L:411 , HOH L:486	binding site for residue ACT L 302
9	AC9	SOFTWARE	ARG A:28 , LYS A:30 , 57S B:301 , SER H:31 , PHE H:32 , TRP H:33 , GLY H:95 , ASP H:96 , HOH H:421 , ARG L:27D , ARG L:34 , LEU L:38 , TYR L:97 , HOH L:439 , HOH L:526	binding site for residue 57S L 303

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:139	-	B:195
5	H:22	-	H:92
6	H:139	-	H:195
7	L:23	-	L:94
8	L:140	-	L:200

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Pro A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Phe B:145	-	Pro B:146
5	Glu B:147	-	Pro B:148
6	Phe H:145	-	Pro H:146
7	Glu H:147	-	Pro H:148
8	Ser L:7	-	Pro L:8
9	Pro L:100	-	Pro L:101
10	Tyr L:146	-	Pro L:147

(no "SAP(SNP)/Variant" information available for 5D6C)

(no "PROSITE Motif" information available for 5D6C)

(no "Exon" information available for 5D6C)

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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....hhhhh...eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d6c A   1 DIQLTQSPDSLAVSLGERATINCKSSQSIFRTSRNKNLLNWYQQRPGQPPRLLIHWASTRKSGVPDRFSGSGFGTDFTLTITSLQAEDVAIYYCQQYFSPPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                     27A|||||                                                                                                                                                                                          
                                                      27B||||                                                                                                                                                                                          
                                                       27C|||                                                                                                                                                                                          
                                                        27D||                                                                                                                                                                                          
                                                         27E|                                                                                                                                                                                          
                                                          27F

Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee...eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh...eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d6c B   1 EVQLVESGGGLVQPGGSLRLSCSASGFSFNSFWMHWVRQVPGKGLVWISFTNNEGTTTAYADSVRGRFIISRDNAKNTLYLEMNNLRGEDTAVYYCARGDGGLDDWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 212
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126|      142       152       162       172       182       192       202       212
                                                                              52A                            82A||                                         126|                                                                               
                                                                                                              82B|                                          133                                                                               
                                                                                                               82C

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee...ee.....eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d6c H   1 EVQLVESGGGLVQPGGSLRLSCSASGFSFNSFWMHWVRQVPGKGLVWISFTNNEGTTTAYADSVRGRFIISRDNAKNTLYLEMNNLRGEDTAVYYCARGDGGLDDWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 218
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206     ||  
                                                                              52A                            82A||                                                                                                                               212|  
                                                                                                              82B|                                                                                                                                216  
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d6c L   1 DIQLTQSPDSLAVSLGERATINCKSSQSIFRTSRNKNLLNWYQQRPGQPPRLLIHWASTRKSGVPDRFSGSGFGTDFTLTITSLQAEDVAIYYCQQYFSPPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 219
                                    10        20       27C||||    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                                                     27A||||||                                                                                                                                                                                         
                                                      27B|||||                                                                                                                                                                                         
                                                       27C||||                                                                                                                                                                                         
                                                        27D|||                                                                                                                                                                                         
                                                         27E||                                                                                                                                                                                         
                                                          27F|                                                                                                                                                                                         
                                                            34

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5D6C)

(no "CATH Domain" information available for 5D6C)

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu B:147 - Pro B:148	[ RasMol ]
		Glu H:147 - Pro H:148	[ RasMol ]
		Phe B:145 - Pro B:146	[ RasMol ]
		Phe H:145 - Pro H:146	[ RasMol ]
		Pro A:94 - Pro A:95	[ RasMol ]
		Pro L:100 - Pro L:101	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:146 - Pro L:147	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (8, 8)

Cis Peptide Bonds (10, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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