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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN FAB VRC38.01, AN HIV-1 V1V2-DIRECTED NEUTRALIZING ANTIBODY ISOLATED FROM DONOR N90
 
Authors :  J. Gorman, P. D. Kwong
Date :  20 Nov 15  (Deposition) - 23 Nov 16  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fab, Hiv-1, V1V2, Env, Antibody, Envelope, Neutralizing, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Cale, J. Gorman, N. A. Radakovich, E. T. Crooks, K. Osawa, T. Tong, J. Li, R. Nagarajan, G. Ozorowski, D. R. Ambrozak, M. Asokan, R. T. Bailer, A. K. Bennici, X. Chen, N. A. Doria-Rose, A. Druz, Y. Feng, M. G. Joyce, M. K. Louder, S. O'Dell, C. Oliver, M. Pancera, M. Connors, T. J. Hope, T. B. Kepler, R. T. Wyatt, A. B. Ward, I. S. Georgiev, P. D. Kwong, J. R. Mascola, J. M. Binley
Virus-Like Particles Identify An Hiv V1V2 Apex-Binding Neutralizing Antibody That Lacks A Protruding Loop.
Immunity V. 46 777 2017
PubMed-ID: 28514685  |  Reference-DOI: 10.1016/J.IMMUNI.2017.04.011

(-) Compounds

Molecule 1 - VRC38.01 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 2 - VRC38.01 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5EWI)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Ser L:7 -Pro L:8
4Thr L:94 -Pro L:95
5Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EWI)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee......eeeeeeeee..eeeeeeeee.....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeee............ee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ewi H    1 EVQLVESGGKLVQPGGSLRLSCEASGESVGDNDMHWVRQVAGKGLEWVSSIGSSGDTYYIDAVKGRFTVSRDKGRNSVYLQMKTLTVGDTGVYFCVRGPESGWFYHYYWGLGVWGRGTTVTVSSASTKGPSVFPLAPSSKGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G|      109       119       129|      143       153       163       173       183       193       203       213 
                                                                                                            82A||               100A|||||||                          129|                                                                                
                                                                                                             82B|                100B||||||                           134                                                                                
                                                                                                              82C                 100C|||||                                                                                                              
                                                                                                                                   100D||||                                                                                                              
                                                                                                                                    100E|||                                                                                                              
                                                                                                                                     100F||                                                                                                              
                                                                                                                                      100G|                                                                                                              
                                                                                                                                       100H                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ewi L    1 DLLMTQSPHSLAVTPGEPASISCRSSQSLLLGNGRNYLDWYVQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGTYFTLKISRVEAEDVGFYYCMEARQTPRLTFGGGTKLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20       27C||      35        45        55        65        75        85        95|      104       114       124       134       144       154       164       174       184       194       204       
                                                     27A||||                                                                  95A                                                                                                                    
                                                      27B|||                                                                                                                                                                                         
                                                       27C||                                                                                                                                                                                         
                                                        27D|                                                                                                                                                                                         
                                                         27E
   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 5EWI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5ewi)
 
  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Thr L:94 - Pro L:95   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  Q6N089_HUMAN | Q6N089
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGKC_HUMAN | P01834: 1a4j 1a4k 1cly 1d5b 1d5i 1d6v 1dfb 1gaf 1hez 1hkl 1hzh 1i7z 1mim 1n0x 1om3 1op3 1op5 1ucb 2ny7 2o5x 2o5y 2o5z 2qqk 2qql 2qqn 2qsc 2r56 2rfx 2vxq 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3cfj 3cfk 3csy 3d0l 3d85 3dvg 3dvn 3eyf 3eyo 3eyq 3iu3 3o11 3qct 3qcu 3qcv 3ru8 3u0w 3u7w 3u7y 3vh8 3wuw 3x11 3x12 4d3c 4d9r 4hix 4nm4 4nm8 4xmp 4xny 4xnz 4xxd 4ydv 5b38 5b39 5c7k 5esv 5esz 5veb 5viy
        Q6N089_HUMAN | Q6N089: 2oqj 3mnv 3qct 3qcu 3qcv 4nm4 4nm8 4nuj 5ug0
UniProtKB/TrEMBL
        Q6N089_HUMAN | Q6N089: 1u6a 3cfj 3cfk 4hpy

(-) Related Entries Specified in the PDB File

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