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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  I2 (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 :  3.00
Chains :  Asym./Biol. Unit :  A,B
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 - I2 HEAVY CHAIN
    Cell Line: HEK 293T
    Chains: A
    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: B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4QHN)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:193

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Gly A:133 -Gly A:134
2Gly A:134 -Thr A:135
3Phe A:146 -Pro A:147
4Glu A:148 -Pro A:149
5Val B:28 -Ala B:29
6Ser B:67 -Gly B:68
7Gly B:68 -Ser B:69
8Leu B:106A-Gly B:107
9Tyr B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QHN)

(-) 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 A from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eee...eeeeeee........eeeeeeeee...eeeeeeee.....eee.......eeeeee....eeeeeee..hhhhheeeeeeeee...............eeeeee.......eeeeeeee........eeeeeeeeee.....eeee.hhh....eee..........eeeeeeeee..........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4qhn A    2 VQLQESGPGVVKSSETLSLTCTVSGGSMGGTYWSWLRLSPGKGLEWIGYIFHTGHTNYNPSLEGRVSISVDTSEDQFSLRLRSVTAADTAVYFCASLPRGQLVNAYFRNWGRGTLVSVTAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    11        21        31        41        51        61        71        81 |||    88        98  |||||103       113       123       133       143       153       163       173       183       193       203       213  
                                                                                                           82A||               100A||||                                                                                                                   
                                                                                                            82B|                100B|||                                                                                                                   
                                                                                                             82C                 100C||                                                                                                                   
                                                                                                                                  100D|                                                                                                                   
                                                                                                                                   100E                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.......eeeee..........eeeee......eeee.............ee.......eeeee...hhhhheeeeeeeee...eeee...eee..........eeeee..hhhhhhh..eeeeeeeeee....eeeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qhn B    3 ELTQPPSVSVSPGQTATITCSGDKVASKNVCWYQVKPGQSPEVVMYENYKRPSGIPDRFSGSKSGSTATLTIRGTQATDEADYYCQVWDSFSTFVFGSGTQVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                  ||13        23        33        43        53        63        73        83        93  |    102    |  111       121       131       141       151       161       171       181       191       201        
                                  9|                                                                                  95A        106A                                                                                                       
                                  11
   Legend:   → Mismatch (orange background)
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    → 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 4QHN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4qhn)
 
  Sites
(no "Sites" information available for 4qhn)
 
  Cis Peptide Bonds
    Glu A:148 - Pro A:149   [ RasMol ]  
    Gly A:133 - Gly A:134   [ RasMol ]  
    Gly A:134 - Thr A:135   [ RasMol ]  
    Gly B:68 - Ser B:69   [ RasMol ]  
    Leu B:106A - Gly B:107   [ RasMol ]  
    Phe A:146 - Pro A:147   [ RasMol ]  
    Ser B:67 - Gly B:68   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
    Val B:28 - Ala B:29   [ RasMol ]  
 

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  4qhn
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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 4qhm

(-) Related Entries Specified in the PDB File

4qhk 4qhl 4qhm