2DD8 - JenaLib

Molecule 1 - IGG HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDZ1.0
	Expression System Strain	:	HB2151
	Expression System Taxid	:	562
	Expression System Vector Type	:	PHAGEMID
	Fragment	:	FAB M396, HEAVY CHAIN
	Gene	:	RECOMBINANT ANTIBODY FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - IGG LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDZ1.0
	Expression System Strain	:	HB2151
	Expression System Taxid	:	562
	Expression System Vector Type	:	PHAGEMID
	Fragment	:	FAB M396, LIGHT CHAIN
	Gene	:	RECOMBINANT ANTIBODY FAB
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - SPIKE GLYCOPROTEIN
	Chains	:	S
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PACGP67A
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	RECEPTOR-BINDING DOMAIN, RESIDUES 317-518
	Gene	:	TOR2
	Organism Scientific	:	SARS CORONAVIRUS
	Organism Taxid	:	227859
	Strain	:	SARS
	Synonym	:	SARS SPIKE, PEPLOMER PROTEIN, E2

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (9, 9)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 9)

Asymmetric Unit (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_014 *	K	344	R	SPIKE_CVHSA	---	---	S	K	344	R
2	UniProt	VAR_SPIKE_CVHSA_015 *	F	360	S	SPIKE_CVHSA	---	---	S	F	360	S
3	UniProt	VAR_SPIKE_CVHSA_016 *	R	426	G	SPIKE_CVHSA	---	---	S	R	426	G
4	UniProt	VAR_SPIKE_CVHSA_017 *	N	437	D	SPIKE_CVHSA	---	---	S	N	437	D
5	UniProt	VAR_SPIKE_CVHSA_018 *	L	472	P	SPIKE_CVHSA	---	---	S	L	472	P
6	UniProt	VAR_SPIKE_CVHSA_019 *	N	479	K	SPIKE_CVHSA	---	---	S	N	479	K
7	UniProt	VAR_SPIKE_CVHSA_020 *	D	480	G	SPIKE_CVHSA	---	---	S	D	480	G
8	UniProt	VAR_SPIKE_CVHSA_021 *	T	487	S	SPIKE_CVHSA	---	---	S	T	487	S
9	UniProt	VAR_SPIKE_CVHSA_022 *	F	501	Y	SPIKE_CVHSA	---	---	S	F	501	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_014 *	K	344	R	SPIKE_CVHSA	---	---	S	K	344	R
2	UniProt	VAR_SPIKE_CVHSA_015 *	F	360	S	SPIKE_CVHSA	---	---	S	F	360	S
3	UniProt	VAR_SPIKE_CVHSA_016 *	R	426	G	SPIKE_CVHSA	---	---	S	R	426	G
4	UniProt	VAR_SPIKE_CVHSA_017 *	N	437	D	SPIKE_CVHSA	---	---	S	N	437	D
5	UniProt	VAR_SPIKE_CVHSA_018 *	L	472	P	SPIKE_CVHSA	---	---	S	L	472	P
6	UniProt	VAR_SPIKE_CVHSA_019 *	N	479	K	SPIKE_CVHSA	---	---	S	N	479	K
7	UniProt	VAR_SPIKE_CVHSA_020 *	D	480	G	SPIKE_CVHSA	---	---	S	D	480	G
8	UniProt	VAR_SPIKE_CVHSA_021 *	T	487	S	SPIKE_CVHSA	---	---	S	T	487	S
9	UniProt	VAR_SPIKE_CVHSA_022 *	F	501	Y	SPIKE_CVHSA	---	---	S	F	501	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_014 *	K	344	R	SPIKE_CVHSA	---	---	S	K	344	R
2	UniProt	VAR_SPIKE_CVHSA_015 *	F	360	S	SPIKE_CVHSA	---	---	S	F	360	S
3	UniProt	VAR_SPIKE_CVHSA_016 *	R	426	G	SPIKE_CVHSA	---	---	S	R	426	G
4	UniProt	VAR_SPIKE_CVHSA_017 *	N	437	D	SPIKE_CVHSA	---	---	S	N	437	D
5	UniProt	VAR_SPIKE_CVHSA_018 *	L	472	P	SPIKE_CVHSA	---	---	S	L	472	P
6	UniProt	VAR_SPIKE_CVHSA_019 *	N	479	K	SPIKE_CVHSA	---	---	S	N	479	K
7	UniProt	VAR_SPIKE_CVHSA_020 *	D	480	G	SPIKE_CVHSA	---	---	S	D	480	G
8	UniProt	VAR_SPIKE_CVHSA_021 *	T	487	S	SPIKE_CVHSA	---	---	S	T	487	S
9	UniProt	VAR_SPIKE_CVHSA_022 *	F	501	Y	SPIKE_CVHSA	---	---	S	F	501	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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 H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains d2dd8h1 H:2-113 Immunoglobulin heavy chain variable domain, VH                                                       d2dd8h2 H:114-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 2dd8H01 H:2-113 Immunoglobulins                                                                                      2dd8H02 H:114-216 Immunoglobulins                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee.........eeeeee......eeeeee.hhhh.eee.hhhh..eeeee.....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2dd8 H    2 VQLQQSGAEVKKPGSSVKVSCKASGGTFSSYTISWVRQAPGQGLEWMGGITPILGIANYAQKFQGRVTITTDESTSTAYMELSSLRSEDTAVYYCARDTVMGGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTSALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    11        21        31        41        51 |      60        70        80  |||   87        97   |   106       116       126       136       146       156       166       176       186       196       206       216
                                                                             52A                            82A||               100A                                                                                                                    
                                                                                                             82B|                                                                                                                                       
                                                                                                              82C

Chain L from PDB  Type:PROTEIN  Length:212
 aligned with Q8N355_HUMAN | Q8N355 from UniProtKB/TrEMBL  Length:234

    Alignment length:214
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
        Q8N355_HUMAN     20 SYVLTQPPSVSVAPGQTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVDAGDEADYYCQLWDSSSDHPVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  233
               SCOP domains -d2dd8l1 L:3-108 Immunoglobulin light chain lambda variable domain, VL-lambda                                 d2dd8l2 L:109-213 Immunoglobulin light chain lambda constant domain, CL-lambda                           SCOP domains
               CATH domains 2dd8L01 L:2-108 Immunoglobulins                                                                               2dd8L02 L:109-213 Immunoglobulins                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee...ee--ee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2dd8 L    2 SYELTQPPSVSVAPGKTARITCGGNNIGSKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDY--VFGTGTKVTVLGQPKANPTVTLFPPSSEEFQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  213
                                    11        21        31        41        51        61        71        81        91    ||  98       108       118       128       138       148       158       168 ||    179       189       199       209    
                                                                                                                        95A| 97                                                                      170|                                         
                                                                                                                          96                                                                          172

Chain S from PDB  Type:PROTEIN  Length:192
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:192
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510  
         SPIKE_CVHSA    321 NLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCG  512
               SCOP domains d2dd8s1 S:321-512 Spike protein S1                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh..........eeeee..ee..hhhhhh.....eeeee..hhhhh...ee.eeeeeeeeee.hhhhhh.....hhhhhhh........eeeeeeehhhhhh........eee....................................eee.......hhhh.eeeeeeeeee.......ee. Sec.struct. author
                 SAPs(SNPs) -----------------------R---------------S-----------------------------------------------------------------G----------D----------------------------------P------KG------S-------------Y----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2dd8 S  321 NLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCG  512
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510

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 (5, 5)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (18, 18)

Asymmetric Unit(hide GO term definitions)

Chain L (Q8N355_HUMAN | Q8N355)

molecular function
	GO:0005515		protein binding		Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

Chain S (SPIKE_CVHSA | P59594)

molecular function
	GO:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0061025	membrane fusion	The membrane organization process that joins two lipid bilayers to form a single membrane.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0046813	receptor-mediated virion attachment to host cell	The process by which a virion attaches to a host cell by binding to a receptor on the host cell surface.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044173	host cell endoplasmic reticulum-Golgi intermediate compartment membrane	The lipid bilayer surrounding any of the compartments of the host cell ER-Golgi intermediate compartment system.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

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	2dd8
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q8N355_HUMAN \| Q8N355
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	SPIKE_CVHSA \| P59594
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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		Disease Information	:	OMIM

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Description

Compounds