4GW1 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CQFD MEDITOPE

Authors :   J. M. Donaldson, C. Zer, K. N. Avery, K. P. Bzymek, D. A. Horne, J. C. Willi

Date :   31 Aug 12 (Deposition) - 09 Oct 13 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.24

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

Keywords :   Igg, Immune System, Egfr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Donaldson, C. Zer, K. N. Avery, K. P. Bzymek, D. A. Horne, J. C. Williams
Identification And Grafting Of A Unique Peptide-Binding Sit In The Fab Framework Of Monoclonal Antibodies.
Proc. Natl. Acad. Sci. Usa V. 110 17456 2013
PubMed-ID: 24101516 | Reference-DOI: 10.1073/PNAS.1307309110

Molecule 1 - FAB LIGHT CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Organism Scientific	:	MUS MUSCULUS,HOMO SAPIENS
	Organism Taxid	:	10090,9606

Molecule 2 - FAB HEAVY CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Organism Scientific	:	MUS MUSCULUS,HOMO SAPIENS
	Organism Taxid	:	10090,9606

Molecule 3 - CQFD MEDITOPE
	Chains	:	E, F
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B			E
Biological Unit 2 (1x)	:			C	D		F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:39 , ARG A:45 , PRO A:59 , ARG A:61 , HOH A:435	BINDING SITE FOR RESIDUE PO4 A 301
2	AC2	SOFTWARE	ARG C:39 , ARG C:45 , PRO C:59 , ARG C:61 , HOH C:426 , HOH C:541	BINDING SITE FOR RESIDUE PO4 C 301
3	AC3	SOFTWARE	SER C:156 , GLY C:157 , HOH C:423 , HOH C:455 , HOH C:475 , HOH C:515 , HOH C:547	BINDING SITE FOR RESIDUE PO4 C 302

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:95
4	B:146	-	B:202
5	C:23	-	C:88
6	C:134	-	C:194
7	D:22	-	D:95
8	D:146	-	D:202
9	E:1	-	E:12
10	F:1	-	F:12

Asymmetric 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:152	-	Pro B:153
5	Glu B:154	-	Pro B:155
6	Ser C:7	-	Pro C:8
7	Trp C:94	-	Pro C:95
8	Tyr C:140	-	Pro C:141
9	Phe D:152	-	Pro D:153
10	Glu D:154	-	Pro D:155

(no "SAP(SNP)/Variant" information available for 4GW1)

(no "PROSITE Motif" information available for 4GW1)

(no "Exon" information available for 4GW1)

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:212
                                                                                                                                                                                                                                                    
               SCOP domains d4gw1a1 A:1-107 automated matches                                                                          d4gw1a2 A:108-212 automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gw1 A   1 DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeeee...eeeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gw1 B   1 QVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4gw1c1 C:1-107 automated matches                                                                          d4gw1c2 C:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gw1 C   1 DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain D from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeeee...eeeeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gw1 D   1 QVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain E from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..ee....ee.. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4gw1 E   1 CQFDLSTRRLKC  12
                                    10

Chain F from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..ee....ee.. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4gw1 F   1 CQFDLSTRRLKC  12
                                    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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Murinae, homo sapiens [TaxId: 39107] (2)

1a	d4gw1a1	A:1-107
1b	d4gw1c1	C:1-107

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Murinae, homo sapiens [TaxId: 39107] (2)

2a	d4gw1a2	A:108-212
2b	d4gw1c2	C:108-213

(no "CATH Domain" information available for 4GW1)

(no "Pfam Domain" information available for 4GW1)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4GW1)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu B:154 - Pro B:155	[ RasMol ]
		Glu D:154 - Pro D:155	[ RasMol ]
		Phe B:152 - Pro B:153	[ RasMol ]
		Phe D:152 - Pro D:153	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]
		Trp A:94 - Pro A:95	[ RasMol ]
		Trp C:94 - Pro C:95	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr C:140 - Pro C:141	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (10, 10)

Cis Peptide Bonds (10, 10)

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SAPs(SNPs)/Variants (0, 0)

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