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(-) Description

Title :  FAB FRAGMENT OF 3D6 IN COMPLEX WITH AMYLOID BETA 1-40
 
Authors :  H. Feinberg, J. W. Saldanha, L. Diep, A. Goel, A. Widom, G. M. Veldman, W. D. Schenk, G. S. Basi
Date :  28 Jan 14  (Deposition) - 11 Jun 14  (Release) - 30 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Antibody, Amyloid Beta Peptide, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Feinberg, J. W. Saldanha, L. Diep, A. Goel, A. Widom, G. M. Veldman, W. I. Weis, D. Schenk, G. S. Basi
Crystal Structure Reveals Conservation Of Amyloid-Beta Conformation Recognized By 3D6 Following Humanization To Bapineuzumab.
Alzheimers Res Ther V. 6 31 2014
PubMed-ID: 25024748  |  Reference-DOI: 10.1186/ALZRT261

(-) Compounds

Molecule 1 - 3D6 FAB ANTIBODY HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - 3D6 FAB ANTIBODY LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - AMYLOID BETA A4 PROTEIN
    Chains: P
    Engineered: YES
    Fragment: UNP RESIDUES 672-711
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 41)

Asymmetric/Biological Unit (3, 41)
No.NameCountTypeFull Name
1CL11Ligand/IonCHLORIDE ION
2IMD3Ligand/IonIMIDAZOLE
3ZN27Ligand/IonZINC ION

(-) Sites  (42, 42)

Asymmetric Unit (42, 42)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP H:213 , HOH H:406BINDING SITE FOR RESIDUE ZN H 301
02AC2SOFTWAREASP H:62 , IMD H:315 , HOH H:402 , HOH H:403BINDING SITE FOR RESIDUE ZN H 302
03AC3SOFTWAREHIS H:170 , ASP L:172 , HOH L:405 , HOH L:407BINDING SITE FOR RESIDUE ZN H 303
04AC4SOFTWAREIMD H:314 , CL H:316 , CL H:317 , HOH H:401BINDING SITE FOR RESIDUE ZN H 304
05AC5SOFTWARECL H:318 , CL H:319 , HOH H:405 , HOH H:518BINDING SITE FOR RESIDUE ZN H 305
06AC6SOFTWAREGLU H:1 , ASP H:179 , HOH H:407 , HOH H:444BINDING SITE FOR RESIDUE ZN H 306
07AC7SOFTWAREARG L:101 , HOH L:474 , HOH L:475 , HOH L:476 , ASP P:1 , PHE P:4 , HOH P:102 , HOH P:105BINDING SITE FOR RESIDUE ZN H 307
08AC8SOFTWARELYS H:65 , IMD H:315 , CL H:320BINDING SITE FOR RESIDUE ZN H 308
09AC9SOFTWAREHOH H:416 , HOH H:478 , PHE P:4BINDING SITE FOR RESIDUE ZN H 309
10BC1SOFTWARETHR H:113 , HOH H:408 , HOH H:409 , HOH H:410 , HOH H:463BINDING SITE FOR RESIDUE ZN H 310
11BC2SOFTWARELYS H:214 , HOH H:452 , HOH H:502BINDING SITE FOR RESIDUE ZN H 311
12BC3SOFTWAREARG H:44 , GLU H:46 , HOH H:414 , HOH H:474BINDING SITE FOR RESIDUE ZN H 312
13BC4SOFTWAREHOH H:411 , HOH H:412 , HOH H:517BINDING SITE FOR RESIDUE ZN H 313
14BC5SOFTWARETHR H:200 , SER H:209 , LYS H:211 , LYS H:215 , ZN H:304 , CL H:316 , CL H:317BINDING SITE FOR RESIDUE IMD H 314
15BC6SOFTWARETYR H:60 , ASP H:62 , ZN H:302 , ZN H:308 , CL H:320 , HOH H:403 , PHE L:99BINDING SITE FOR RESIDUE IMD H 315
16BC7SOFTWAREPRO H:206 , ZN H:304 , IMD H:314BINDING SITE FOR RESIDUE CL H 316
17BC8SOFTWAREZN H:304 , IMD H:314BINDING SITE FOR RESIDUE CL H 317
18BC9SOFTWAREASN H:161 , SER H:162 , ASN H:202 , ZN H:305 , CL H:319BINDING SITE FOR RESIDUE CL H 318
19CC1SOFTWARELYS H:211 , ASP H:213 , ZN H:305 , CL H:318BINDING SITE FOR RESIDUE CL H 319
20CC2SOFTWARETYR H:59 , TYR H:60 , LYS H:65 , ZN H:308 , IMD H:315BINDING SITE FOR RESIDUE CL H 320
21CC3SOFTWARETYR L:1 , HIS L:98BINDING SITE FOR RESIDUE ZN L 301
22CC4SOFTWAREHIS L:194 , CL L:319 , CL L:320 , HOH L:524BINDING SITE FOR RESIDUE ZN L 302
23CC5SOFTWAREASP L:115 , HOH L:408BINDING SITE FOR RESIDUE ZN L 303
24CC6SOFTWAREHIS L:203 , CL L:316 , CL L:317 , HOH L:406BINDING SITE FOR RESIDUE ZN L 304
25CC7SOFTWAREIMD L:315 , HOH L:401 , HOH L:402 , HOH L:403BINDING SITE FOR RESIDUE ZN L 305
26CC8SOFTWAREASP L:170 , CL L:318 , HOH L:409 , HOH L:410BINDING SITE FOR RESIDUE ZN L 306
27CC9SOFTWAREHOH L:465BINDING SITE FOR RESIDUE ZN L 307
28DC1SOFTWARELYS L:154 , GLU L:200 , HOH L:502 , HOH L:523BINDING SITE FOR RESIDUE ZN L 308
29DC2SOFTWAREGLU L:84 , HOH L:436BINDING SITE FOR RESIDUE ZN L 309
30DC3SOFTWAREHOH L:430 , HOH L:473 , HOH L:522BINDING SITE FOR RESIDUE ZN L 310
31DC4SOFTWAREGLY L:157 , SER L:196 , CL L:321 , HOH L:497 , HOH L:521BINDING SITE FOR RESIDUE ZN L 311
32DC5SOFTWAREASP L:175BINDING SITE FOR RESIDUE ZN L 312
33DC6SOFTWAREASP L:31 , HOH L:411 , ARG P:5BINDING SITE FOR RESIDUE ZN L 313
34DC7SOFTWAREHIS H:170 , ASN L:143 , ASP L:172 , HOH L:404 , HOH L:407BINDING SITE FOR RESIDUE ZN L 314
35DC8SOFTWARELEU L:9 , GLY L:105 , GLY L:106 , ZN L:305BINDING SITE FOR RESIDUE IMD L 315
36DC9SOFTWAREALA L:116 , ALA L:117 , HIS L:203 , ZN L:304 , CL L:317BINDING SITE FOR RESIDUE CL L 316
37EC1SOFTWAREHIS L:203 , ZN L:304 , CL L:316BINDING SITE FOR RESIDUE CL L 317
38EC2SOFTWAREASP L:170 , ZN L:306BINDING SITE FOR RESIDUE CL L 318
39EC3SOFTWAREHIS L:194 , ZN L:302 , CL L:320BINDING SITE FOR RESIDUE CL L 319
40EC4SOFTWAREHIS L:194 , ZN L:302 , CL L:319 , HOH L:500BINDING SITE FOR RESIDUE CL L 320
41EC5SOFTWAREASP L:156 , GLY L:157 , SER L:196 , THR L:198 , ZN L:311BINDING SITE FOR RESIDUE CL L 321
42EC6SOFTWAREMET H:34 , SER H:35 , SER H:50 , ILE H:51 , ARG H:52 , TYR H:59 , TYR H:99 , SER H:105 , SER H:106 , ZN H:307 , ZN H:309 , HOH H:478 , ASP L:31 , TYR L:37 , TRP L:94 , GLY L:96 , THR L:97 , HIS L:98 , ARG L:101 , ZN L:313 , HOH L:413 , HOH L:474 , HOH L:475 , HOH L:476 , HOH P:101 , HOH P:102 , HOH P:103 , HOH P:104 , HOH P:105BINDING SITE FOR CHAIN P OF AMYLOID BETA A4 PROTEIN

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:146 -H:201
3L:23 -L:93
4L:139 -L:199

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe H:152 -Pro H:153
2Glu H:154 -Pro H:155
3Trp H:194 -Pro H:195
4Thr L:7 -Pro L:8
5Phe L:99 -Pro L:100
6Tyr L:145 -Pro L:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ONG)

(-) Sequences/Alignments

Asymmetric/Biological 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 H from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ong H   1 EVKLVESGGGLVKPGASLKLSCAASGFTFSNYGMSWVRQNSDKRLEWVASIRSGGGRTYYSDNVKGRFTISRENAKNTLYLQMSSLKSEDTALYYCVRYDSGSSDYWGQGTTVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 219
                                    10        20        30        40        50        60        70        80        90       100|      112       122       132|      149       159       169       179       189       199       209       219
                                                                                                                             100|                          132|                                                                               
                                                                                                                              103                           140                                                                               


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ong L   1 YVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRIEAEDLGLYYCWQGTHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSPIVKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   ||  212    
                                                                                                                                                                                                                                     204|         
                                                                                                                                                                                                                                      207         


Chain P from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author hhhhh Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4ong P   1 DAEFR   5
   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 4ONG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (111, 111)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        A4_HUMAN | P05067: 1aap 1amb 1amc 1aml 1ba4 1ba6 1bjb 1bjc 1brc 1ca0 1hz3 1iyt 1mwp 1owt 1qcm 1qwp 1qxc 1qyt 1taw 1tkn 1uo7 1uo8 1uoa 1uoi 1x11 1z0q 1ze7 1ze9 1zjd 2beg 2bom 2bp4 2fjz 2fk1 2fk2 2fk3 2fkl 2fma 2g47 2ipu 2lfm 2llm 2lmn 2lmo 2lmp 2lmq 2lnq 2loh 2lp1 2lz3 2lz4 2m4j 2m9r 2m9s 2mgt 2mj1 2mpz 2mvx 2mxu 2nao 2otk 2r0w 2wk3 2y29 2y2a 2y3j 2y3k 2y3l 3ayu 3bae 3bkj 3dxc 3dxd 3dxe 3gci 3ifl 3ifn 3ifo 3ifp 3jq5 3jql 3jti 3ktm 3l33 3l81 3moq 3mxc 3mxy 3nyj 3nyl 3ovj 3ow9 3sv1 3u0t 3umh 3umi 3umk 4hix 4jfn 4m1c 4mdr 4mvi 4mvk 4mvl 4nge 4ojf 4onf 4pqd 4pwq 4xxd 5aef 5am8 5amb 5buo 5c67 5csz 5how 5hox 5hoy 5kk3 5kna 5myo

(-) Related Entries Specified in the PDB File

4onf