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(-) Description

Title :  I3.1 (UNBOUND) FROM CH103 LINEAGE
 
Authors :  D. Fera, S. C. Harrison
Date :  28 May 14  (Deposition) - 11 Jun 14  (Release) - 30 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.23
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  E,F  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Fab Fragment, Hiv-1, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Fera, A. G. Schmidt, B. F. Haynes, F. Gao, H. X. Liao, T. B. Kepler, S. C. Harrison
Affinity Maturation In An Hiv Broadly Neutralizing B-Cell Lineage Through Reorientation Of Variable Domains.
Proc. Natl. Acad. Sci. Usa V. 111 10275 2014
PubMed-ID: 24982157  |  Reference-DOI: 10.1073/PNAS.1409954111

(-) Compounds

Molecule 1 - I3 HEAVY CHAIN
    Cell Line: HEK 293T
    Chains: A, E, C, G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293T
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC-8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - I2 LIGHT CHAIN
    Cell Line: HEK 293T
    Chains: F, B, D, H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293T
    Expression System Common: HUMAN
    Expression System Plasmid: PVRC-8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):     EF  
Biological Unit 3 (1x):   CD    
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4QHM)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:193
5C:22 -C:92
6C:140 -C:196
7D:23 -D:88
8D:134 -D:193
9E:22 -E:92
10E:140 -E:196
11F:23 -F:88
12F:134 -F:193
13G:22 -G:92
14G:140 -G:196
15H:23 -H:88
16H:134 -H:193

(-) Cis Peptide Bonds  (20, 20)

Asymmetric Unit
No.Residues
1Gln A:105 -Gly A:106
2Phe A:146 -Pro A:147
3Glu A:148 -Pro A:149
4Gln E:105 -Gly E:106
5Phe E:146 -Pro E:147
6Glu E:148 -Pro E:149
7Gln C:105 -Gly C:106
8Phe C:146 -Pro C:147
9Glu C:148 -Pro C:149
10Gln G:105 -Gly G:106
11Phe G:146 -Pro G:147
12Glu G:148 -Pro G:149
13Leu F:106A-Gly F:107
14Tyr F:140 -Pro F:141
15Leu B:106A-Gly B:107
16Tyr B:140 -Pro B:141
17Leu D:106A-Gly D:107
18Tyr D:140 -Pro D:141
19Leu H:106A-Gly H:107
20Tyr H:140 -Pro H:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QHM)

(-) 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:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee.....eeeeee.......eeeeeeee.....eeeeeee.....eee........eeeee....eeeee....hhhhheeeeeeeee...............eeeeee.......eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee...eeeeeeeeeee........eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhm A    1 QVQLQESGPGLVKSSETLSLTCTVSGGSMGGYYWSWLRQSPVKGLEWIGYIFHTGHTNYNPSLESRVTVSVDTSENQFSLRLRSVTAADTAVYYCASLPRGQLVNAFFDNWGQGTLVTVASASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122    || 138       148       158       168       178       188       198       208       
                                                                                                            82A||               100A||||                        127|                                                                                 
                                                                                                             82B|                100B|||                         134                                                                                 
                                                                                                              82C                 100C||                                                                                                             
                                                                                                                                   100D|                                                                                                             
                                                                                                                                    100E                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee......eeeee........eeeeeee..eeeeeee..............eeeee..eeeee....hhhhheeeeeeee.....ee....eeeee........eeeee..hhhhhhh..eeeeeeeeee....eeeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhm B    2 YELTQPPSVSVSPGQTATITCSGDKVASKNVCWYQVKPGQSPEVVMYENYKRPSGIPDRFSGSKSGSTATLTIRGTQATDEADYYCQVWDSFSTFVFGSGTQVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       170       180       190       200         
                                   9|                                                                                  95A        106A                                                                                                       
                                   11                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee.....eeeeee.......eeeeeeeee...eeeeeeee.....eee........eeee.....eeeee....hhhhheeeeeeeee...............eeeeee.......eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhm C    1 QVQLQESGPGLVKSSETLSLTCTVSGGSMGGYYWSWLRQSPVKGLEWIGYIFHTGHTNYNPSLESRVTVSVDTSENQFSLRLRSVTAADTAVYYCASLPRGQLVNAFFDNWGQGTLVTVASASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122    || 138       148       158       168       178       188       198       208       
                                                                                                            82A||               100A||||                        127|                                                                                 
                                                                                                             82B|                100B|||                         134                                                                                 
                                                                                                              82C                 100C||                                                                                                             
                                                                                                                                   100D|                                                                                                             
                                                                                                                                    100E                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee......eeeee........eeeeeee..eeeeeee..............eeeee..eeeee....hhhhheeeeeeee.....ee....eeeee........eeeee..hhhhhhh..eeeeeeeeee....eeeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhm D    2 YELTQPPSVSVSPGQTATITCSGDKVASKNVCWYQVKPGQSPEVVMYENYKRPSGIPDRFSGSKSGSTATLTIRGTQATDEADYYCQVWDSFSTFVFGSGTQVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       170       180       190       200         
                                   9|                                                                                  95A        106A                                                                                                       
                                   11                                                                                                                                                                                                        


Chain E from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee.....eeeeee.......eeeeeeeee...eeeeeeee.....eee........eeeee....eeeee....hhhhheeeeeeeee...............eeeeee.......eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhm E    1 QVQLQESGPGLVKSSETLSLTCTVSGGSMGGYYWSWLRQSPVKGLEWIGYIFHTGHTNYNPSLESRVTVSVDTSENQFSLRLRSVTAADTAVYYCASLPRGQLVNAFFDNWGQGTLVTVASASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122    || 138       148       158       168       178       188       198       208       
                                                                                                            82A||               100A||||                        127|                                                                                 
                                                                                                             82B|                100B|||                         134                                                                                 
                                                                                                              82C                 100C||                                                                                                             
                                                                                                                                   100D|                                                                                                             
                                                                                                                                    100E                                                                                                             


Chain F from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee......eeeee........eeeeeee..eeeeeee..............eeeee..eeeee....hhhhheeeeeeee.....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee....eeeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhm F    2 YELTQPPSVSVSPGQTATITCSGDKVASKNVCWYQVKPGQSPEVVMYENYKRPSGIPDRFSGSKSGSTATLTIRGTQATDEADYYCQVWDSFSTFVFGSGTQVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       170       180       190       200         
                                   9|                                                                                  95A        106A                                                                                                       
                                   11                                                                                                                                                                                                        


Chain G from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eee.....eeeeeee......eeeeeeee.....eeeeeee.....eee........eeee.....eeeee....hhhhheeeeeeeee...............eeeeee.......eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhm G    1 QVQLQESGPGLVKSSETLSLTCTVSGGSMGGYYWSWLRQSPVKGLEWIGYIFHTGHTNYNPSLESRVTVSVDTSENQFSLRLRSVTAADTAVYYCASLPRGQLVNAFFDNWGQGTLVTVASASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122    || 138       148       158       168       178       188       198       208       
                                                                                                            82A||               100A||||                        127|                                                                                 
                                                                                                             82B|                100B|||                         134                                                                                 
                                                                                                              82C                 100C||                                                                                                             
                                                                                                                                   100D|                                                                                                             
                                                                                                                                    100E                                                                                                             


Chain H from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee......eeeee........eeeeeee..eeeeeee..............eeeee..eeeee....hhhhheeeeeeee.....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee....eeeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhm H    2 YELTQPPSVSVSPGQTATITCSGDKVASKNVCWYQVKPGQSPEVVMYENYKRPSGIPDRFSGSKSGSTATLTIRGTQATDEADYYCQVWDSFSTFVFGSGTQVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       170       180       190       200         
                                   9|                                                                                  95A        106A                                                                                                       
                                   11
   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 4QHM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4QHM)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4qhm)
 
  Cis Peptide Bonds
    Gln A:105 - Gly A:106   [ RasMol ]  
    Gln C:105 - Gly C:106   [ RasMol ]  
    Gln E:105 - Gly E:106   [ RasMol ]  
    Gln G:105 - Gly G:106   [ RasMol ]  
    Glu A:148 - Pro A:149   [ RasMol ]  
    Glu C:148 - Pro C:149   [ RasMol ]  
    Glu E:148 - Pro E:149   [ RasMol ]  
    Glu G:148 - Pro G:149   [ RasMol ]  
    Leu B:106A - Gly B:107   [ RasMol ]  
    Leu D:106A - Gly D:107   [ RasMol ]  
    Leu F:106A - Gly F:107   [ RasMol ]  
    Leu H:106A - Gly H:107   [ RasMol ]  
    Phe A:146 - Pro A:147   [ RasMol ]  
    Phe C:146 - Pro C:147   [ RasMol ]  
    Phe E:146 - Pro E:147   [ RasMol ]  
    Phe G:146 - Pro G:147   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
    Tyr D:140 - Pro D:141   [ RasMol ]  
    Tyr F:140 - Pro F:141   [ RasMol ]  
    Tyr H:140 - Pro H:141   [ RasMol ]  
 
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  4qhm
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 Related Entries

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

UniProtKB/TrEMBL
        Q6GMX6_HUMAN | Q6GMX6: 1bey 1za6 2jix 3b2u 3b2v 3d0l 3zl4 4d9l 4fqq 4lkx 4npy 4qhk 4qhl 4qhn

(-) Related Entries Specified in the PDB File

4qhk 4qhl 4qhn