5D1X - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   ISDB NEAT2 BOUND BY D4-30

Authors :   X. Deng

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

Method :   X-RAY DIFFRACTION

Resolution :   3.21

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

Keywords :   Isdb, Neat2, 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 - D4-30 LIGHT CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - D4-30 HEAVY CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	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 Taxid	:	9606
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - P5 LIGHT CHAIN
	Chains	:	D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	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, SAUSA300_1028
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS (STRAIN USA300)
	Organism Taxid	:	367830
	Strain	:	USA300
	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 5D1X)

(no "Site" information available for 5D1X)

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	D:23	-	D:88
7	D:134	-	D:194

Asymmetric/Biological Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Trp A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Phe B:150	-	Pro B:151
5	Thr D:7	-	Pro D:8
6	Tyr D:140	-	Pro D:141
7	His E:369	-	Pro E:370

(no "SAP(SNP)/Variant" information available for 5D1X)

(no "PROSITE Motif" information available for 5D1X)

(no "Exon" information available for 5D1X)

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:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeee....eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d1x A    1 DIVMTQSPLSLPVTLGQPASISCSSAQSLVHSDGDSYLTWFHQRPGQSPRRLIYKVSIRDAGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQATHWPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30|||||   35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                        30A||||                                                                                                                                                                                       
                                                         30B|||                                                                                                                                                                                       
                                                          30C||                                                                                                                                                                                       
                                                           30D|                                                                                                                                                                                       
                                                            30E

Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeeeee..hhhhh.eeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeeee..hhhhheeeeeee.......ee...eeeee........eeeee.......eeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeee..........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d1x B    1 QVQLVQSGSEVKKPGSSVTLSCKASGDTFNTHTYSWVRQAPGQRLEWIGGIMPIFAASKSAPHLQDRLTITANKATRTAYMELTSLTSDDSGVYYCARDGRGALQYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  217
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       120       130|      145       155       165       175       185       195       205       215  
                                                                              52A                            82A||                             114|        130|                                                                                 
                                                                                                              82B|                              119         136                                                                                 
                                                                                                               82C

Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....ee..............eeeeee.....eeeeeee................ee.......eeeeee....eeeeee...hhhhh.eeeeee.............eeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d1x C    6 ESGGGLVQPGGSLTLSCAASGLIFSDSTMHWVRQASGRGLEWVARIRSKANNYATSSDKSATAYLASVKGRFTISRDDSKDTTFLEMSSLKIEDTAVYYCIASSTTGWYVREDFDYWGHGTLVTVSS  113
                                    15        25        35        45       52C||||||| 55        65        75       82C        92      100B||||   106       
                                                                         52A||||||52J                            82A||               100A|||||             
                                                                          52B|||||||                              82B|                100B||||             
                                                                           52C||||||                               82C                 100C|||             
                                                                            52D|||||                                                    100D||             
                                                                             52E||||                                                     100E|             
                                                                              52F|||                                                      100F             
                                                                               52G||                                                                       
                                                                                52H|                                                                       
                                                                                 52I

Chain D from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......eeeeeee....hhh.eeeee.......eeeee...ee.......eeeee....eeeee...hhhhh..eeeeee.....eee....eee................hhhhhhh................ee......eeee.......eeee...hhhhhhh.......ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d1x D    1 EIVLTQTPATLSLTPGERATLTCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLSISRLEPEDFAVYYCLHYGTSPMYFFGRGTVLDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWSGNSQESVTEQSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVT  206
                                    10        20        30|       39        49        59        69        79        89      | 98       108       118       128       138       148|      165||     179       189       199       
                                                        30A                                                               95A                                                  148|       166|                                   
                                                                                                                                                                                156        171

Chain E from PDB  Type:PROTEIN  Length:115
                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.eeee.......hhhhh.eeeeeeeee....eeeeeee.hhh.eeeeee.....eeeeee....eeeeeee......eeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                5d1x E  341 KMTDLQDTKYVVYESVENNESMMDTFVKHPIKTGMLNGKKYMVMETTNDDYWKDFMVEGQRVRTISKDAKNNTRTIIFPYVEGKTLYDAIVKVHVKTIDYDGQYHVRIVDKEAFT  455
                                   350       360       370       380       390       400       410       420       430       440       450

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 5D1X)

(no "CATH Domain" information available for 5D1X)

(no "Pfam Domain" information available for 5D1X)

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 5d1x)

	Sites
(no "Sites" information available for 5d1x)

	Cis Peptide Bonds
		His E:369 - Pro E:370	[ RasMol ]
		Phe B:150 - Pro B:151	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Thr D:7 - Pro D:8	[ RasMol ]
		Trp A:94 - Pro A:95	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr D:140 - Pro D:141	[ RasMol ]

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	5d1x
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	ISDB_STAA8 \| Q2FZF0	:	5d1q 5d1z

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (7, 7)

Cis Peptide Bonds (7, 7)

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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