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(-) Description

Title :  CRYSTAL STRUCTURE OF 10E8V4 FAB IN COMPLEX WITH AN HIV-1 GP41 PEPTIDE.
 
Authors :  G. Ofek, Y. D. Kwon, W. Caruso, P. D. Kwong
Date :  10 Mar 16  (Deposition) - 20 Apr 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,H,L,P
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  H,L,P  (1x)
Keywords :  Immunoglobulin, Mper, Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. D. Kwon, I. S. Georgiev, G. Ofek, B. Zhang, M. Asokan, R. T. Bailer, A. Bao, W. Caruso, X. Chen, M. Choe, A. Druz, S. Y. Ko, M. K. Louder, K. Mckee, S. O'Dell, A. Pegu, R. S. Rudicell, W. Shi, K. Wang, Y. Yang, M. Alger, M. F. Bender, K. Carlton, J. W. Cooper, J. Blinn, J. Eudailey, K. Lloyd, R. Parks, S. M. Alam, B. F. Haynes, N. N. Padte, J. Yu, D. D. Ho, J. Huang, M. Connors, R. M. Schwartz, J. R. Mascola, P. D. Kwong
Optimization Of The Solubility Of Hiv-1-Neutralizing Antibody 10E8 Through Somatic Variation And Structure-Based Design.
J. Virol. V. 90 5899 2016
PubMed-ID: 27053554  |  Reference-DOI: 10.1128/JVI.03246-15

(-) Compounds

Molecule 1 - 10E8V4 HEAVY CHAIN
    Chains: A, H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: EXPI 293S
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: IGHG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FRAGMENT ANTIGEN-BINDING
 
Molecule 2 - 10E8V4 LIGHT CHAIN
    Chains: B, L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: EXPI 293S
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: IGLC2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FRAGMENT ANTIGEN-BINDING
 
Molecule 3 - GP41 MPER PEPTIDE
    Chains: C, P
    Engineered: YES
    Fragment: UNP RESIDUES 645-673
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCHLP
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    HLP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5IQ9)

(-) Sites  (0, 0)

(no "Site" information available for 5IQ9)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:135 -B:194
5H:22 -H:92
6H:140 -H:196
7L:23 -L:88
8L:135 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Pro A:100F-Pro A:100G
2Phe A:146 -Pro A:147
3Glu A:148 -Pro A:149
4Tyr B:141 -Pro B:142
5Pro H:100F-Pro H:100G
6Phe H:146 -Pro H:147
7Glu H:148 -Pro H:149
8Tyr L:141 -Pro L:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IQ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IQ9)

(-) Exons   (0, 0)

(no "Exon" information available for 5IQ9)

(-) 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:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee..........eeeeeee...eeeee........eeeeeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5iq9 A    1 EVRLVESGGGLVKPGGSLRLSCSASGFDFDNAWMTWVRQPPGKGLEWVGRITGPGEGWSVDYAESVKGRFTISRDNTKNTLYLEMNNVRTEDTGYYFCARTGKYYDFWSGYPPGEEYFQDWGQGTLVIVSSASTKGPSVFPLAPSSKTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||102       112       122      |137       147       157       167       177       187       197       207       
                                                                              52A||                            82A||               100A|||||100J||                          129|                                                                               
                                                                               52B|                             82B|                100B|||||100K|                           135                                                                               
                                                                                52C                              82C                 100C|||||100L                                                                                                             
                                                                                                                                      100D|||||                                                                                                                
                                                                                                                                       100E||||                                                                                                                
                                                                                                                                        100F|||                                                                                                                
                                                                                                                                         100G||                                                                                                                
                                                                                                                                          100H|                                                                                                                
                                                                                                                                           100I                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..eeeee....eeeeee.hhhhh...eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeeee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5iq9 B    2 SELTQDPAVSVALKQTVTITCRGDSLRSHYASWYQKKPGQAPVLLFYGKNNRPSGIPDRFSGSASGNRASLTITGAQAEDEADYYCSSRDKSGSRLSVFGGGTKLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  209
                                   |12        22        32        42        52        62        72        82        92   |||  99       109       119       129       139       149       159       169       179       189       199       209
                                   9|                                                                                  95A||                                                                                                                  
                                   11                                                                                   95B|                                                                                                                  
                                                                                                                         95C                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:18
                                                   
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                5iq9 C  667 ASLWNWFDITNWLWYIRR  684
                                   676        


Chain H from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee..........eeeeeee...eeeee........eeeeeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh....eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5iq9 H    1 EVRLVESGGGLVKPGGSLRLSCSASGFDFDNAWMTWVRQPPGKGLEWVGRITGPGEGWSVDYAESVKGRFTISRDNTKNTLYLEMNNVRTEDTGYYFCARTGKYYDFWSGYPPGEEYFQDWGQGTLVIVSSASTKGPSVFPLAPSSKTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||102       112       122      |137       147       157       167       177       187       197       207       
                                                                              52A||                            82A||               100A|||||100J||                          129|                                                                               
                                                                               52B|                             82B|                100B|||||100K|                           135                                                                               
                                                                                52C                              82C                 100C|||||100L                                                                                                             
                                                                                                                                      100D|||||                                                                                                                
                                                                                                                                       100E||||                                                                                                                
                                                                                                                                        100F|||                                                                                                                
                                                                                                                                         100G||                                                                                                                
                                                                                                                                          100H|                                                                                                                
                                                                                                                                           100I                                                                                                                


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..eeee.....eeeeee.hhhhh...eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhh....eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5iq9 L    2 SELTQDPAVSVALKQTVTITCRGDSLRSHYASWYQKKPGQAPVLLFYGKNNRPSGIPDRFSGSASGNRASLTITGAQAEDEADYYCSSRDKSGSRLSVFGGGTKLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  209
                                   |12        22        32        42        52        62        72        82        92   |||  99       109       119       129       139       149       159       169       179       189       199       209
                                   9|                                                                                  95A||                                                                                                                  
                                   11                                                                                   95B|                                                                                                                  
                                                                                                                         95C                                                                                                                  


Chain P from PDB  Type:PROTEIN  Length:18
                                                   
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                5iq9 P  667 ASLWNWFDITNWLWYIRR  684
                                   676
   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 5IQ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IQ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IQ9)

(-) Gene Ontology  (38, 57)

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  Cis Peptide Bonds
    Glu A:148 - Pro A:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe A:146 - Pro A:147   [ RasMol ]  
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  Q1HSF8_9HIV1 | Q1HSF8
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGHG1_HUMAN | P01857: 1aj7 1aqk 1axs 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2i5y 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2osl 2qad 2ql1 2qqk 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bm7 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4n 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xmp 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e
        IGLC2_HUMAN | P0DOY2: 1jvk 1lil 1zvo 2jb5 2jb6 3c2a 3tv3 3twc 3tyg 4eow 4lld 4llm 4llq 4llu 4llw 4lly 4o58 4o5i 5d9q 5iq7
        IGLC3_HUMAN | P0DOY3: 1aqk 3tv3 3twc 3tyg 4lld 4llm 4o58 4o5i 4o5l 4r26 4r2g 5d9q 5iq7 7fab

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5IQ9)