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(-) Description

Title :  CETUXIMAB FAB IN COMPLEX WITH CQA(PH)2DLSTRRLKC PEPTIDE
 
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 :  2.48
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (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

(-) Compounds

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
    Engineered: YES
    Expression System: UNIDENTIFIED
    Expression System Taxid: 32644
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 3 - CETUXIMAB FAB HEAVY CHAIN
    Chains: D
    Engineered: YES
    Expression System: UNIDENTIFIED
    Expression System Taxid: 32644
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 4 - CYCLIC MEDITOPE CQA(PH)2DLSTRRLKC
    Chains: E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
12GX2Mod. Amino AcidBETA-PHENYL-L-PHENYLALANINE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4PO45Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
12GX1Mod. Amino AcidBETA-PHENYL-L-PHENYLALANINE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
12GX1Mod. Amino AcidBETA-PHENYL-L-PHENYLALANINE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA-1Mod. Amino AcidPYROGLUTAMIC ACID
4PO43Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:39 , ARG A:45 , PRO A:59 , ARG A:61 , GLU A:81 , HOH A:412 , HOH A:424 , HOH A:447binding site for residue PO4 A 301
2AC2SOFTWAREGLU A:165 , ASP A:167 , VAL B:169 , HIS B:170 , HOH B:405 , HOH B:406 , HOH B:465binding site for residue PO4 B 302
3AC3SOFTWAREARG C:39 , ARG C:45 , PRO C:59 , ARG C:61 , GLU C:81 , HOH C:401 , HOH C:406 , HOH C:420binding site for residue PO4 C 301
4AC4SOFTWAREGLU C:165 , ASP C:167 , VAL D:169 , HIS D:170 , HOH D:407 , HOH D:412 , HOH D:421binding site for residue PO4 D 302
5AC5SOFTWAREASN D:205 , LYS D:207 , ASN D:210 , LYS D:212binding site for residue PO4 D 303
6AC6SOFTWARELYS B:43 , ASN B:88 , HOH B:492binding site for Mono-Saccharide NAG B 301 bound to ASN B 88
7AC7SOFTWARELYS D:43 , ASN D:88 , HOH D:406 , HOH D:430binding site for Mono-Saccharide NAG D 301 bound to ASN D 88

(-) SS Bonds  (10, 10)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Trp A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:152 -Pro B:153
5Glu B:154 -Pro B:155
6Ser C:7 -Pro C:8
7Trp C:94 -Pro C:95
8Tyr C:140 -Pro C:141
9Phe D:152 -Pro D:153
10Glu D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T1L)

(-) Exons   (0, 0)

(no "Exon" information available for 5T1L)

(-) 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 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...ee.......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
                 5t1l 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: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
                 5t1l B   1 xVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS 221
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130  ||   145       155       165       175       185       195       205       215      
                            1-PCA                                                                                                                             133|                                                                                  
                                                                                                                                                               139                                                                                  


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......eeeee...ee.......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
                 5t1l 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
                 5t1l D   1 QVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  144       154       164       174       184       194       204       214      
                                                                                                                                                               134|                                                                                 
                                                                                                                                                                139                                                                                 


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
                 5t1l E   1 CQfDLSTRRLKC  12
                              |     10  
                              3-2GX     


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
                 5t1l F   1 CQfDLSTRRLKC  12
                              |     10  
                              3-2GX
   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  (0, 0)

(no "SCOP Domain" information available for 5T1L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T1L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T1L)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5T1L)

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  5t1l
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 Related Entries

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(-) Related Entries Specified in the PDB File

4gw1 4iwe 5etu 5euk 5f88 5ff6 5i2i 5iop 5ir1 5itf 5iv2 5ivz 5t1k 5t1m 5th2