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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN 4E10 FAB IN COMPLEX WITH ITS PEPTIDE EPITOPE ON HIV-1 GP41: CRYSTALS CRYOPROTECTED WITH SN-GLYCEROL 3-PHOSPHATE
 
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 :  1.63
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Hiv-1 Gp41 Mper, 4E10 Fab, Lipid Membrane, 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
    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
    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 3 - MODIFIED FRAGMENT OF HIV-1 GLYCOPROTEIN (GP41) INCLUDING THE MPER REGION 671-683
    Chains: P
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
141H1Mod. Amino Acid(BETAS)-BETA-METHYL-L-PHENYLALANINE
2G3P2Ligand/IonSN-GLYCEROL-3-PHOSPHATE
3HAI3Ligand/IonCYCLOHEXYLAMMONIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY L:9 , TYR L:87 , GLN L:100 , GLY L:101 , HOH L:691binding site for residue HAI L 301
2AC2SOFTWAREGLY H:27 , SER H:28 , PHE H:29 , SER H:30 , SER H:76 , HOH H:569 , HOH H:672 , HOH H:691 , HOH H:692binding site for residue G3P H 301
3AC3SOFTWARETHR H:57 , TYR H:59 , HOH H:454 , HOH H:668 , LYS L:188 , HIS L:189binding site for residue G3P H 302
4AC4SOFTWARETHR H:70 , TYR H:79 , GLU H:81binding site for residue HAI H 303
5AC5SOFTWARELEU H:53 , LEU H:54 , THR H:55 , ILE H:56 , LEU P:679 , LYS P:683 , HOH P:801binding site for residue HAI P 701

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (4, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XC1)

(-) Exons   (0, 0)

(no "Exon" information available for 4XC1)

(-) 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:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xc1 H    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126|      145       156||     171       182       192       205       215      |227
                                                                              52A                            82A||               100A|||||100J                       126|               154|||    169|      180|               200||              222|  
                                                                                                              82B|                100B|||||||                         136                156||     171       182                203|               225  
                                                                                                               82C                 100C||||||                                             157|                                   205                    
                                                                                                                                    100D|||||                                              162                                                          
                                                                                                                                     100E||||                                                                                                           
                                                                                                                                      100F|||                                                                                                           
                                                                                                                                       100G||                                                                                                           
                                                                                                                                        100H|                                                                                                           
                                                                                                                                         100I                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xc1 L    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 P from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                4xc1 P  671 NWxDITNWLWYIKKK  685
                              |    680     
                            673-41H
   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 4XC1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XC1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XC1)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1MN | P05877: 1acy 1ai1 1f58 1ggi 1k5m 1nak 1niz 1nj0 1q1j 2b0s 2qsc 3e6h 3go1 3mlw 3mlx 3uji 4m1d 4xaw 4xbe 4xc3 4xcf 4xmk

(-) Related Entries Specified in the PDB File

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