5T1M - JenaLib

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Title :   CETUXIMAB FAB IN COMPLEX WITH CQYDLSTRRLKC

Authors :   K. P. Bzymek, J. C. Williams

Date :   19 Aug 16 (Deposition) - 26 Oct 16 (Release) - 09 Nov 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.53

Chains :   Asym. Unit : A,B,C,D,E,F,H
Biol. Unit 1: A,B,E  (1x)
Biol. Unit 2: C,D,F  (1x)
Biol. Unit 3: H  (1x)

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

Reference :   K. P. Bzymek, K. A. Avery, Y. Ma, D. A. Horne, J. C. Williams
Natural And Non-Natural Amino-Acid Side-Chain Substitutions Affinity And Diffraction Studies Of Meditope-Fab Complexes
Acta Crystallogr. , Sect. F V. 72 831 2016
PubMed: search | Reference-DOI: 10.1107/S2053230X16015612

Molecule 1 - CETUXIMAB FAB LIGHT CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	UNIDENTIFIED
	Expression System Taxid	:	32644
	Organism Scientific	:	MUS MUSCULUS, HOMO SAPIENS
	Organism Taxid	:	10090, 9606

Molecule 2 - CETUXIMAB FAB HEAVY CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	UNIDENTIFIED
	Expression System Taxid	:	32644
	Organism Scientific	:	MUS MUSCULUS, HOMO SAPIENS
	Organism Taxid	:	10090, 9606

Molecule 3 - CYCLIC PEPTIDE CQYDLSTRRLKC
	Chains	:	E, F, H
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	H
Biological Unit 1 (1x)	:	A	B			E
Biological Unit 2 (1x)	:			C	D		F
Biological Unit 3 (1x)	:							H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID
3	PO4	6	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	PCA	-1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:39 , ARG A:45 , PRO A:59 , ARG A:61 , GLU A:81 , HOH A:415 , HOH A:431	binding site for residue PO4 A 301
2	AC2	SOFTWARE	GLU A:165 , ASP A:167 , HIS B:170 , HOH B:408 , HOH B:412 , HOH B:434 , HOH B:448	binding site for residue PO4 B 302
3	AC3	SOFTWARE	ASN B:205 , ASN B:210	binding site for residue PO4 B 303
4	AC4	SOFTWARE	ARG C:39 , ARG C:45 , PRO C:59 , ARG C:61 , GLU C:81 , HOH C:405 , HOH C:413	binding site for residue PO4 C 301
5	AC5	SOFTWARE	GLU C:165 , ASP C:167 , HOH C:447 , HIS D:170 , HOH D:402 , HOH D:428 , HOH D:437 , HOH D:445	binding site for residue PO4 D 302
6	AC6	SOFTWARE	ASN D:205 , LYS D:207 , ASN D:210 , LYS D:212	binding site for residue PO4 D 303
7	AC7	SOFTWARE	LYS B:43 , ASN B:88 , HOH B:426	binding site for Mono-Saccharide NAG B 301 bound to ASN B 88
8	AC8	SOFTWARE	ARG D:38 , SER D:40 , GLY D:42 , LYS D:43 , ASN D:88 , HOH D:431 , HOH D:459	binding site for Mono-Saccharide NAG D 301 bound to ASN D 88

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
11	H:1	-	H: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	Gly D:139	-	Gly D:140
10	Phe D:152	-	Pro D:153
11	Glu D:154	-	Pro D:155

(no "SAP(SNP)/Variant" information available for 5T1M)

(no "PROSITE Motif" information available for 5T1M)

(no "Exon" information available for 5T1M)

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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t1m A   1 DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGA 213
                                    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:219
                                                                                                                                                                                                                                                           
               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.hhhhhh..eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t1m B   1 xVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 220
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130   ||  141       151       161       171       181       191       201       211         
                            1-PCA                                                                                                                              134|                                                                                    
                                                                                                                                                                136

Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t1m C   1 DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGA 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:216
                                                                                                                                                                                                                                                        
               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......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t1m D   1 xVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 220
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130  ||   144       154       164       174       184       194       204       214      
                            1-PCA                                                                                                                             133|                                                                                  
                                                                                                                                                               138

Chain E from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .eee....eee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5t1m E   1 CQYDLSTRRLKC  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 .eee....eee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5t1m F   1 CQYDLSTRRLKC  12
                                    10

Chain H from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .eee....eee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5t1m H   1 CQYDLSTRRLKC  12
                                    10

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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	Cis Peptide Bonds
		Glu B:154 - Pro B:155	[ RasMol ]
		Glu D:154 - Pro D:155	[ RasMol ]
		Gly D:139 - Gly D:140	[ 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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	5t1m
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (8, 8)

SS Bonds (11, 11)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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