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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN 4E10 FAB CRYSTALIZED IN THE PRESENCE OF PHOSPHATIDYLCHOLINE (06:0 PC); C2 SPACE GROUP
 
Authors :  A. Irimia, R. L. Stanfield, I. A. Wilson
Date :  17 Dec 14  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.93
Chains :  Asym. Unit :  A,B,C,D,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  4E10 Fab Anti Hiv-1 Gp41, Phosphatidylcholine, Membrane Lipid, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Irimia, A. Sarkar, R. L. Stanfield, I. A. Wilson
Crystallographic Identification Of Lipid As An Integral Component Of The Epitope Of Hiv Broadly Neutralizing Antibody 4E10.
Immunity V. 44 21 2016
PubMed-ID: 26777395  |  Reference-DOI: 10.1016/J.IMMUNI.2015.12.001

(-) Compounds

Molecule 1 - 4E10 FAB LIGHT CHAIN
    Chains: L, B, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 FREESTYLE
    Expression System Plasmid: PDR12
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 4E10 FAB HEAVY CHAIN
    Chains: H, A, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 FREESTYLE
    Expression System Plasmid: PDR12
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHL
Biological Unit 1 (1x):     HL
Biological Unit 2 (1x): AB    
Biological Unit 3 (1x):   CD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4XCE)

(-) Sites  (0, 0)

(no "Site" information available for 4XCE)

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:142 -A:208
3B:23 -B:88
4B:134 -B:194
5C:22 -C:92
6C:142 -C:208
7D:23 -D:88
8D:134 -D:194
9H:22 -H:92
10H:142 -H:208
11L:23 -L:88
12L:134 -L:194

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Tyr L:186 -Glu L:187
4Leu H:54 -Thr H:55
5Phe H:148 -Pro H:149
6Glu H:150 -Pro H:151
7Ser B:7 -Pro B:8
8Tyr B:140 -Pro B:141
9Phe A:148 -Pro A:149
10Glu A:150 -Pro A:151
11Ser D:7 -Pro D:8
12Tyr D:140 -Pro D:141
13Gly C:100D-Lys C:100E
14Phe C:148 -Pro C:149
15Glu C:150 -Pro C:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XCE)

(-) 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:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeeeehhhheeee.......eeee......eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xce A    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126|||    140       150   ||||165   ||  176   ||  187       197  |||  210       220 ||  
                                                                              52A                            82A||               100A|||||100J                       126|||                  154|||    169|      180|               200||              222|  
                                                                                                              82B|                100B|||||||                         129||                   156||     171       182                203|               225  
                                                                                                               82C                 100C||||||                          130|                    157|                                   205                    
                                                                                                                                    100D|||||                           133                     162                                                          
                                                                                                                                     100E||||                                                                                                                
                                                                                                                                      100F|||                                                                                                                
                                                                                                                                       100G||                                                                                                                
                                                                                                                                        100H|                                                                                                                
                                                                                                                                         100I                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xce B    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
                                                     27A                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee.....eeeeeee.........eeeeee......eeeeee......eee.......eeee......eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xce C    2 VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  230
                                    11        21        31        41        51 |      60        70        80  |||   87        97   |||100G|||    107       117       127|      144       154|||    169|      180|      191       203|      214       226    
                                                                             52A                            82A||               100A|||||100J                        127|                154|||    169|      180|               200||              222|     
                                                                                                             82B|                100B|||||||                          135                 156||     171       182                203|               225     
                                                                                                              82C                 100C||||||                                               157|                                   205                       
                                                                                                                                   100D|||||                                                162                                                             
                                                                                                                                    100E||||                                                                                                                
                                                                                                                                     100F|||                                                                                                                
                                                                                                                                      100G||                                                                                                                
                                                                                                                                       100H|                                                                                                                
                                                                                                                                        100I                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xce D    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
                                                     27A                                                                                                                                                                                          


Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeee......eee.hhhh..eeee......eeeeee...hhhhheeeeeeeeeee......eeeeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh...eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xce H    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGATSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  230
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126||     144       154|||  ||171       182       192       205       215      |227   
                                                                              52A                            82A||               100A|||||100J                        127|               154|||  || ||      180|               200||              222|     
                                                                                                              82B|                100B|||||||                          136                156||  || ||       182                203|               225     
                                                                                                               82C                 100C||||||                                              157|  || ||                           205                       
                                                                                                                                    100D|||||                                               162  || ||                                                     
                                                                                                                                     100E||||                                                  165| ||                                                     
                                                                                                                                      100F|||                                                   167 ||                                                     
                                                                                                                                       100G||                                                     169|                                                     
                                                                                                                                        100H|                                                      171                                                     
                                                                                                                                         100I                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeee........eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xce L    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       |29        39        49        59        69        79        89  ||   101       111       121       131       141       151       161       171       181       191       201       211  
                                                     27A                                                               92|                                                                                                                      
                                                                                                                        95
   Legend:   → Mismatch (orange background)
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  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 4XCE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  Cis Peptide Bonds
    Glu A:150 - Pro A:151   [ RasMol ]  
    Glu C:150 - Pro C:151   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
    Gly C:100D - Lys C:100E  [ RasMol ]  
    Leu H:54 - Thr H:55   [ RasMol ]  
    Phe A:148 - Pro A:149   [ RasMol ]  
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    Phe H:148 - Pro H:149   [ RasMol ]  
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    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
    Tyr D:140 - Pro D:141   [ RasMol ]  
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    Tyr L:186 - Glu L:187   [ RasMol ]  
 
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  4xce
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 Related Entries

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(-) Related Entries Specified in the PDB File

4xaw 4xbe 4xbg 4xbp 4xc1 4xc3 4xcc 4xcf 4xcn 4xcy