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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIV-1 BROADLY NEUTRALIZING ANTIBODY 2F5 IN COMPLEX WITH THE GP41 FP-MPER HYB3K CONSTRUCT 514GIGALFLGFLGAAGS528KK-AHX-655KNEQELLELDKWASLWN671 SOAKED IN PEG/2-PROPANOL SOLUTION
 
Authors :  S. Bryson, J. P. Julien, E. F. Pai
Date :  11 Jul 08  (Deposition) - 07 Oct 08  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hiv-1, 2F5, Gp41, Nmab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Julien, S. Bryson, J. L. Nieva, E. F. Pai
Structural Details Of Hiv-1 Recognition By The Broadly Neutralizing Monoclonal Antibody 2F5: Epitope Conformation, Antigen-Recognition Loop Mobility, And Anion-Binding Site.
J. Mol. Biol. V. 384 377 2008
PubMed-ID: 18824005  |  Reference-DOI: 10.1016/J.JMB.2008.09.024

(-) Compounds

Molecule 1 - 2F5 FAB' LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System Cell Line: HYBRIDOMA CELLS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 2F5 FAB' HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System Cell Line: HYBRIDOMA CELLS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GP41 PEPTIDE EPITOPE
    Chains: C
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED BY FMOC CHEMISTRY. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN THE HUMAN IMMUNODEFICIENCY VIRUS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:160 , SER A:162 , SER A:176 , SER A:177 , THR A:178 , PHE B:166 , PRO B:167 , SER B:177 , LEU B:178 , SER B:179BINDING SITE FOR RESIDUE GOL A 3731

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DRQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DRQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3DRQ)

(-) 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:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3drqA01 A:1-107 Immunoglobulins                                                                            3drqA02 A:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee..ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3drq A    1 ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRPEDFATYYCQQLHFYPHTFGGGTRVDVRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYECEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3drqB01 B:1-113 Immunoglobulins                                                                                            3drqB02 B:114-213 Immunoglobulins                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeeeee...........ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3drq B    1 RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQVVLVMTRVSPVDTATYFCAHRRGPTGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEP  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95    ||100N       110       120     ||137       147       157       167       177       187       197       207      
                                                             35A|                                             82A||              100I|||||                       126|                                                                               
                                                              35B                                              82B|               100J||||                        134                                                                               
                                                                                                                82C                100K|||                                                                                                          
                                                                                                                                    100L||                                                                                                          
                                                                                                                                     100M|                                                                                                          
                                                                                                                                      100N                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .ee..... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                3drq C    2 LELDKWAS    9
   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 3DRQ)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DRQ)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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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 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 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e
        Q6PYX1_HUMAN | Q6PYX1: 3c2s 4j12
UniProtKB/TrEMBL
        Q6PYX1_HUMAN | Q6PYX1: 1ce1 1um4 1um5 1um6 2rcj 3bqu 3dro 3eo0 4nhg 4nhh 4qgt

(-) Related Entries Specified in the PDB File

2p8m 3d0l 3dro 3drt 3drv