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(-) Description

Title :  CRYSTAL STRUCTURE OF A FAB BINDING TO EXTRACELLULAR DOMAIN 5 OF CADHERIN-6
 
Authors :  X. Zhu, C. U. Bialucha, A. London, K. Clark, T. Hu
Date :  04 Apr 17  (Deposition) - 07 Jun 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B,H,L,X,Y
Biol. Unit 1:  A,B,X  (1x)
Biol. Unit 2:  H,L,Y  (1x)
Keywords :  Antibody, Cell Adhesion, Antibody-Drug Conjugate, Cancer, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. U. Bialucha, S. D. Collins, X. Li, P. Saxena, X. Zhang, C. Durr, B. Lafont, P. Prieur, Y. Shim, R. Mosher, D. Lee, L. Ostrom, T. Hu, S. Bilic, I. Liric Rajlic, V. Capka, W. Jiang, J. P. Wagner, G. Elliott A. Veloso, J. C. Piel, M. M. Flaherty, K. G. Mansfield, E. K. Meseck, T. Rubic-Schneider, A. Serdakowski London, W. R. Tschantz, M. Kurz, D. Nguyen, A. Bourret, M. J. Meyer, J. E. Faris, M. J. Janatpour, V. W. Chan, N. C. Yoder, K. C. Catcott, M. A. Mcshea, X. Sun, H. Gao, J. Williams, F. Hofmann, J. A. Engelman, S. A. Ettenberg, W. R. Sellers E. Lees
Discovery And Optimization Of Hkt288, A Cadherin-6 Targetin Adc For The Treatment Of Ovarian And Renal Cancer.
Cancer Discov 2017
PubMed-ID: 28526733  |  Reference-DOI: 10.1158/2159-8290.CD-16-1414

(-) Compounds

Molecule 1 - ANTI-CDH6 FAB HEAVY CHAIN
    Chains: A, H
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTI-CDH6 FAB LIGHT CHAIN
    Chains: B, L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - CADHERIN-6
    Chains: X, Y
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: KIDNEY CADHERIN,K-CADHERIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABHLXY
Biological Unit 1 (1x): AB  X 
Biological Unit 2 (1x):   HL Y

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1A2G4Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2SIN1Ligand/IonSUCCINIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2SIN1Ligand/IonSUCCINIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2SIN-1Ligand/IonSUCCINIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:59 , TYR A:60 , LYS A:65 , SER B:14 , ASP B:17 , PRO B:95 , TYR X:575binding site for residue SIN A 1001
2AC2SOFTWAREALA X:528 , GLU X:530 , SER X:579 , THR X:581 , A2G X:2002binding site for Mono-Saccharide A2G X 2001 bound to THR X 581
3AC3SOFTWARETHR X:581 , GLY X:582 , THR X:583 , A2G X:2001binding site for Mono-Saccharide A2G X 2002 bound to THR X 583
4AC4SOFTWAREALA Y:528 , GLU Y:530 , SER Y:579 , THR Y:581 , A2G Y:2002binding site for Mono-Saccharide A2G Y 2001 bound to THR Y 581
5AC5SOFTWARETHR Y:581 , THR Y:583 , A2G Y:2001binding site for Mono-Saccharide A2G Y 2002 bound to THR Y 583

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:145 -A:201
3A:221 -B:215
4B:23 -B:88
5B:135 -B:195
6H:22 -H:96
7H:145 -H:201
8H:221 -L:215
9L:23 -L:88
10L:135 -L:195
11X:497 -X:591
12Y:497 -Y:591

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Phe A:151 -Pro A:152
2Glu A:153 -Pro A:154
3Ser B:7 -Pro B:8
4Phe B:94 -Pro B:95
5Pro B:95 -Pro B:96
6Tyr B:141 -Pro B:142
7Phe H:151 -Pro H:152
8Glu H:153 -Pro H:154
9Ser L:7 -Pro L:8
10Phe L:94 -Pro L:95
11Pro L:95 -Pro L:96
12Tyr L:141 -Pro L:142
13Tyr X:575 -Pro X:576
14Tyr Y:575 -Pro Y:576

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VEB)

(-) 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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee........eeeee....eeeeee...hhhhheeeeeeeee...eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5veb A   1 QVQLLESGGGLVQPGGSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVSVISGSGSNTGYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARQWGSYAFDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee...eeeeee......eeeee...eee......eeeeeeeeeeeeee...hhhhheeeeeee.......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5veb B   1 DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAVSTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSGTFPPTTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee........eeeee....eeeeee...hhhhheeeeeeeee...eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5veb H   1 QVQLLESGGGLVQPGGSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVSVISGSGSNTGYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARQWGSYAFDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee...eeeeee......eeeee...eee......eeeeeeeeeeeeee...hhhhheeeeeee.......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5veb L   1 DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAVSTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSGTFPPTTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain X from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eeeeeeee...........eeee.........eeeee....eeeeee...........eeeeeeeee.......eeeeeeeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5veb X 494 TFVCEKAKADQLIQTLHAVDKDDPYSGHQFSFSLAPEAASGSNFTIQDNKDNTAGILTRKNGYNRHEMSTYLLPVVISDNDYPVQSSTGTVTVRVCACPLEVLFQ 614
                                   503       513       523       533       543       553       563       573       583       609     
                                                                                                                           591|      
                                                                                                                            608      


Chain Y from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......eeeeeeee...........eeee.........eeeee....eeeeee...........eeeeeeeee.......eeeeeeeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5veb Y 492 YETFVCEKAKADQLIQTLHAVDKDDPYSGHQFSFSLAPEAASGSNFTIQDNKDNTAGILTRKNGYNRHEMSTYLLPVVISDNDYPVQSSTGTVTVRVCACPLEVLFQ 614
                                   501       511       521       531       541       551       561       571       581       591|      
                                                                                                                             591|      
                                                                                                                              608
   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 5VEB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 35)

Asymmetric Unit(hide GO term definitions)

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  5veb
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  CADH6_HUMAN | P55285
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  IGKC_HUMAN | P01834
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  S6B291_HUMAN | S6B291
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IGKC_HUMAN | P01834: 1a4j 1a4k 1cly 1d5b 1d5i 1d6v 1dfb 1gaf 1hez 1hkl 1hzh 1i7z 1mim 1n0x 1om3 1op3 1op5 1ucb 2ny7 2o5x 2o5y 2o5z 2qqk 2qql 2qqn 2qsc 2r56 2rfx 2vxq 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3cfj 3cfk 3csy 3d0l 3d85 3dvg 3dvn 3eyf 3eyo 3eyq 3iu3 3o11 3qct 3qcu 3qcv 3ru8 3u0w 3u7w 3u7y 3vh8 3wuw 3x11 3x12 4d3c 4d9r 4hix 4nm4 4nm8 4xmp 4xny 4xnz 4xxd 4ydv 5b38 5b39 5c7k 5esv 5esz 5ewi 5viy
        S6B291_HUMAN | S6B291: 3mnw 3mnz 4eow 5c7k 5cus 5d9q 5vic 5vig 5viy 5vj6 5vob 5voc 5vod
UniProtKB/TrEMBL
        S6B291_HUMAN | S6B291: 4llw 4lly 4oqt 4ydv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5VEB)