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Biological Unit 2 (Jmol Viewer)

Title :   FC HETERODIMER DESIGN 8.1 L368V/Y407A + T366V/K409F

Authors :   S. Atwell, A. Leaver-Fay, K. J. Froning, H. Aldaz, A. Pustilnik, F. Lu, F R. Yuan, S. H. Dhanani, A. K. Chamberlain, J. R. Fitchett, B. Gutierrez J. Hendle, E. Secrist, S. J. Demarest, B. Kuhlman

Date :   01 Sep 15 (Deposition) - 30 Mar 16 (Release) - 27 Apr 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Heterodimer, Immunoglobulin, Ch3, Fc, Bispecific Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Leaver-Fay, K. J. Froning, S. Atwell, H. Aldaz, A. Pustilnik, F. Lu, F. Huang, R. Yuan, S. Hassanali, A. K. Chamberlain, J. R. Fitchett, S. J. Demarest, B. Kuhlman
Computationally Designed Bispecific Antibodies Using Negative State Repertoires.
Structure V. 24 641 2016
PubMed-ID: 26996964 | Reference-DOI: 10.1016/J.STR.2016.02.013

Molecule 1 - IG GAMMA-1 CHAIN C REGION
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 104-330
	Gene	:	IGHG1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - IG GAMMA-1 CHAIN C REGION
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 104-330
	Gene	:	IGHG1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - FC-III PEPTIDE
	Chains	:	C, F
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Other Details	:	CPC SCIENTIFIC INC., SUNNYVALE CA
	Synthetic	:	YES

		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	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 33)

No.	Name	Count	Type	Full Name
1	BMA	4	Ligand/Ion	BETA-D-MANNOSE
2	FUC	4	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	4	Ligand/Ion	BETA-D-GALACTOSE
4	IOD	1	Ligand/Ion	IODIDE ION
5	MAN	8	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (5, 16)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	IOD	-1	Ligand/Ion	IODIDE ION
5	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (6, 17)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	IOD	1	Ligand/Ion	IODIDE ION
5	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:629	binding site for residue IOD D 509
2	AC2	SOFTWARE	PHE A:241 , PHE A:243 , PRO A:244 , LYS A:246 , GLU A:258 , THR A:260 , VAL A:264 , ASP A:265 , GLN A:295 , ASN A:297 , ARG A:301 , HOH A:602 , HOH A:635 , HOH A:637 , ILE D:253	binding site for Poly-Saccharide residues NAG A 501 through MAN A 508 bound to ASN A 297
3	AC3	SOFTWARE	PHE B:241 , PHE B:243 , PRO B:244 , PRO B:245 , LYS B:246 , ASP B:249 , GLU B:258 , THR B:260 , VAL B:264 , ASP B:265 , GLN B:295 , ASN B:297 , ARG B:301 , ALA E:253	binding site for Poly-Saccharide residues NAG B 501 through FUC B 508 bound to ASN B 297
4	AC4	SOFTWARE	ILE A:253 , PHE D:241 , PHE D:243 , PRO D:244 , LYS D:246 , GLU D:258 , THR D:260 , VAL D:264 , ASP D:265 , GLN D:295 , ASN D:297 , THR D:299 , ARG D:301 , HOH D:602 , HOH D:621 , HOH D:637 , HOH D:649	binding site for Poly-Saccharide residues NAG D 501 through MAN D 508 bound to ASN D 297
5	AC5	SOFTWARE	PHE E:241 , PHE E:243 , PRO E:244 , PRO E:245 , LYS E:246 , ASP E:249 , GLU E:258 , THR E:260 , VAL E:264 , ASP E:265 , GLN E:295 , ASN E:297 , ARG E:301 , HOH E:622	binding site for Poly-Saccharide residues NAG E 501 through FUC E 508 bound to ASN E 297

Asymmetric Unit

No.	Residues
1	A:261	-	A:321
2	A:367	-	A:425
3	B:261	-	B:321
4	B:367	-	B:425
5	C:2	-	C:12
6	D:261	-	D:321
7	D:367	-	D:425
8	E:261	-	E:321
9	E:367	-	E:425
10	F:2	-	F:12

Asymmetric Unit

No.	Residues
1	Tyr A:373	-	Pro A:374
2	Tyr B:373	-	Pro B:374
3	Tyr D:373	-	Pro D:374
4	Tyr E:373	-	Pro E:374

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

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

(no "Exon" information available for 5DJC)

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:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhh.....eeeeeeeeee......eeeeee..eee...ee...ee....eeeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhh...eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5djc A 237 GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCVVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLASKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 443
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436

Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhh.....eeeeeeeeee......eeeeee..eee...ee...eee...eeeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee....hhhhh.eeeeeeeeeee.....eeeee........eee...ee.....eeeeeeeeeehhhhhh..eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5djc B 237 GPSVFLFPPKPKDTLEASRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLVCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSFLTVDKSRWQQNVFSCSVMHEALHNAYTQKSLSL 443
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416  ||   427       437      
                                                                                                                                                                                                                419|                      
                                                                                                                                                                                                                 421

Chain C from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5djc C   1 DCAWHLGELVWCT  13
                                    10

Chain D from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhh.....eeeeeeeeee......eeeeee..eee...ee...ee....eeeeeeeee.hhhhhhhh..eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5djc D 237 GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCVVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLASKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 443
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436

Chain E from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..eee...ee...ee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhh...eeeeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeeeeehhhhhh...eeeeee...hhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5djc E 237 GPSVFLFPPKPKDTLEASRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLVCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSFLTVDKSRWQQGNVFSCSVMHEALHNAYTQKSLSL 443
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436

Chain F from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5djc F   1 DCAWHLGELVWCT  13
                                    10

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 5DJC)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Tyr A:373 - Pro A:374	[ RasMol ]
		Tyr B:373 - Pro B:374	[ RasMol ]
		Tyr D:373 - Pro D:374	[ RasMol ]
		Tyr E:373 - Pro E:374	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 33)

Sites (5, 5)

SS Bonds (10, 10)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (20, 20)

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