5D1Q - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   ISDB NEAT2 BOUND BY CLONE D2-06

Authors :   X. Deng

Date :   04 Aug 15 (Deposition) - 10 Aug 16 (Release) - 07 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.22

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   Isdb Neat2, Igvh1-69, Germline Encoded, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. A. Yeung, D. Foletti, X. Deng, Y. Abdiche, P. Strop, J. Glanville, S. Pitts, K. Lindquist, P. D. Sundar, M. Sirota, A. Hasa-Moreno, A. Pham, J. Melton Witt, I. Ni, J. Pons, D. Shelton, A. Rajpal, J. Chaparro-Riggers
Germline-Encoded Neutralization Of A Staphylococcus Aureus Virulence Factor By The Human Antibody Repertoire.
Nat Commun V. 7 13376 2016
PubMed-ID: 27857134 | Reference-DOI: 10.1038/NCOMMS13376

Molecule 1 - D2-06 LIGHT CHAIN
	Cell	:	MEMORY B CELL
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - D2-06 HEAVY CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - P5 HEAVY CHAIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - P5 LIGHT CHAIN
	Chains	:	D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 5 - IRON-REGULATED SURFACE DETERMINANT PROTEIN B
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21-GOLD(DE3)PLYSS AG
	Expression System Taxid	:	866768
	Gene	:	ISDB, FRPB, SASJ, SIRH, SAB0993C
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS (STRAIN BOVINE RF122 / ET3-1)
	Organism Taxid	:	273036
	Strain	:	BOVINE RF122 / ET3-1
	Synonym	:	FUR-REGULATED PROTEIN B,STAPHYLOCOCCAL IRON-REGULATED PROTEIN H,STAPHYLOCOCCUS AUREUS SURFACE PROTEIN J

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 5D1Q)

(no "Site" information available for 5D1Q)

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:144	-	B:200
5	C:22	-	C:92
6	C:144	-	C:200
7	D:23	-	D:88
8	D:134	-	D:194

Asymmetric/Biological Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Phe A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Pro B:97	-	Pro B:98
5	Phe B:150	-	Pro B:151
6	Glu B:152	-	Pro B:153
7	Phe C:150	-	Pro C:151
8	Glu C:152	-	Pro C:153
9	Ser D:7	-	Pro D:8
10	Tyr D:140	-	Pro D:141
11	Ser D:203	-	Pro D:204
12	His E:369	-	Pro E:370

(no "SAP(SNP)/Variant" information available for 5D1Q)

(no "PROSITE Motif" information available for 5D1Q)

(no "Exon" information available for 5D1Q)

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)
	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:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeee...eeeeee.........eeeeee...........eeeee.......eeeee..hhhhhhhheeeeeeeeeee....ee..eee........eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d1q A    1 DIQLTQSPSSVSASVGDRITITCRASQDISNWVAWYQQKPGKAPKLLIYSASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANTFPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eee.....eeeeeee.........eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee.....eeeeeeeeee....eee.hhhhh.....ee...ee.....eeeeeeeee.............eee....eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5d1q B    1 QVQLVQSGAEVKKPASSVKVSCQASGGSFSTRTISWLRQAPGQGLEWMGGISPIFGAANYAQRFQGRVTITADKSTSTAYMELTSLTSEDTAVYYCARDRPPGAQFDTWGQGTLVTVSSASTKGPSVFPLAPSSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  220
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114|      128   ||  144       154       164       174       184       194       204       214      
                                                                              52A                            82A||               100A|           114|          132|                                                                                 
                                                                                                              82B|                100B            119           139                                                                                 
                                                                                                               82C

Chain C from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee.......eeeeeee.....eeeeeee...............eee.hhhh...eeeee....eeeeeee..hhhhheeeeeeee............ee...eeeee........eeeee.........eeeeeeeeeee.................eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d1q C    1 EVQLVESGGGLVQPGGSLTLSCAASGLIFSDSTMHWVRQASGRGLEWVARIRSKANNYATSSDKSATAYLASVKGRFTISRDDSKDTTFLEMSSLKIEDTAVYYCIASSTTGWYVREDFDYWGHGTLVTVSSASTKGPSVFPLAPSSKSTSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  217
                                    10        20        30        40        50  |||||52H||      60        70        80  |||   87        97   ||||101       111  ||   125       135||     146       156       166       176       186       196       206       216 
                                                                              52A||||||52J                            82A||               100A|||||           114|              136|                                                                               
                                                                               52B|||||||                              82B|                100B||||            119               138                                                                               
                                                                                52C||||||                               82C                 100C|||                                                                                                                
                                                                                 52D|||||                                                    100D||                                                                                                                
                                                                                  52E||||                                                     100E|                                                                                                                
                                                                                   52F|||                                                      100F                                                                                                                
                                                                                    52G||                                                                                                                                                                          
                                                                                     52H|                                                                                                                                                                          
                                                                                      52I

Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeeee.....eee...eeeee........eeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee....eeee.........eeeeeeeee..........eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d1q D    1 EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLSISRLEPEDFAVYYCLHYGTSPMYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30|       39        49        59        69        79        89      | 98       108       118       128       138       148       158       168       178       188       198       208    
                                                        30A                                                               95A

Chain E from PDB  Type:PROTEIN  Length:118
                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeee.............eeeeeeeeee..eeeeeeee.hhh.eeeeee..ee.eeeeee....eeeeeee......eeeeeeeeeehhhheeeeeeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                5d1q E  339 PGKMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFTK  456
                                   348       358       368       378       388       398       408       418       428       438       448

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 '\|'

(no "SCOP Domain" information available for 5D1Q)

(no "CATH Domain" information available for 5D1Q)

(no "Pfam Domain" information available for 5D1Q)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5d1q)

	Sites
(no "Sites" information available for 5d1q)

	Cis Peptide Bonds
		Glu B:152 - Pro B:153	[ RasMol ]
		Glu C:152 - Pro C:153	[ RasMol ]
		His E:369 - Pro E:370	[ RasMol ]
		Phe A:94 - Pro A:95	[ RasMol ]
		Phe B:150 - Pro B:151	[ RasMol ]
		Phe C:150 - Pro C:151	[ RasMol ]
		Pro B:97 - Pro B:98	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser D:203 - Pro D:204	[ RasMol ]
		Ser D:7 - Pro D:8	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr D:140 - Pro D:141	[ RasMol ]

Jmol
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	5d1q
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	ISDB_STAA8 \| Q2FZF0	:	5d1x 5d1z

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (7, 14)

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