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(-) Description

Title :  CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U12 IN COMPLEX WITH HIV-1 YU2 GP120
 
Authors :  P. Acharya, P. D. Kwong
Date :  21 Apr 13  (Deposition) - 19 Jun 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,R
Keywords :  Viral Protein-Peptide Complex, Hiv-1, Gp120, Yu2, Cd4 Mimic, M48U12, Viral Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Morellato-Castillo, P. Acharya, O. Combes, J. Michiels, A. Descours, O. H. Ramos, Y. Yang, G. Vanham, K. K. Arien, P. D. Kwong, L. Martin, P. Kessler
Interfacial Cavity Filling To Optimize Cd4-Mimetic Miniprotein Interactions With Hiv-1 Surface Glycoprotein.
J. Med. Chem. V. 56 5033 2013
PubMed-ID: 23710622  |  Reference-DOI: 10.1021/JM4002988

(-) Compounds

Molecule 1 - HIV-1 YU2 GP120
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Gene: GP120
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: YU2
 
Molecule 2 - M48U12
    Chains: R
    Engineered: YES
    Other Details: DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVDERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD,E REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD,
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1DPR1Mod. Amino AcidD-PROLINE
2MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NH21Mod. Amino AcidAMINO GROUP
5U3X1Mod. Amino Acid4-[(CYCLOHEXYLMETHYL)AMINO]-L-PHENYLALANINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS R:19 , ALA R:20 , THR R:22 , U3X R:23 , HOH R:603BINDING SITE FOR RESIDUE DPR R 21
2AC2SOFTWAREASN A:92 , ASN A:276 , THR A:278 , ASN A:279 , HOH A:617 , HOH A:712 , HOH A:820BINDING SITE FOR RESIDUE NAG A 501
3AC3SOFTWAREASN A:234 , THR A:236 , SER A:274BINDING SITE FOR RESIDUE NAG A 502
4AC4SOFTWARELYS A:85 , ASN A:229 , THR A:240 , ASN A:241BINDING SITE FOR RESIDUE NAG A 503
5AC5SOFTWAREGLU A:211 , PRO A:212 , LEU A:261 , ASN A:262 , CYS A:445 , SER A:446 , SER A:447 , NAG A:508 , HOH A:639 , HOH A:649 , HOH A:667BINDING SITE FOR RESIDUE NAG A 504
6AC6SOFTWAREGLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLU A:290 , GLN A:344 , GLU A:351 , HOH A:652 , HOH A:819BINDING SITE FOR RESIDUE NAG A 505
7AC7SOFTWAREPRO A:79 , ASN A:80 , ASN A:295 , LEU A:333 , ASN A:413 , ARG A:444 , HOH A:790BINDING SITE FOR RESIDUE NAG A 506
8AC8SOFTWAREASN A:386 , THR A:388 , HOH A:650 , HOH A:709 , HOH A:816 , HOH A:817BINDING SITE FOR RESIDUE NAG A 507
9AC9SOFTWARESER A:291 , ASN A:448 , NAG A:504 , HOH A:786BINDING SITE FOR RESIDUE NAG A 508

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:74
2A:119 -A:205
3A:218 -A:247
4A:228 -A:239
5A:296 -A:331
6A:378 -A:445
7A:385 -A:418
8R:6 -R:24
9R:10 -R:26

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KA2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KA2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KA2)

(-) Exons   (0, 0)

(no "Exon" information available for 4KA2)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......hhhhhhhhhheee.......eee....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhhh......eeeeeeeee.eee......eee........eeeeeeeeeeeeee.....eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ka2 A  44 VWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGNGTEIFRPGGGDMRDNWRSELYKYKVVKIE 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348       358       368       378       388       412       422       432       442       452      |465       475       485       
                                                                                                          124|                                                                                                    301|                                                                     396|                                             459|                             
                                                                                                           198                                                                                                     324                                                                      411                                              463                             


Chain R from PDB  Type:PROTEIN  Length:28
                                                            
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 4ka2 R   1 xNLHFCQLRCKSLGLLGRCAxTfCACVx  28
                            |       10        20| |    |
                            1-MPT              21-DPR  |
                                                 23-U3X|
                                                      28-NH2
   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 4KA2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KA2)

(-) Gene Ontology  (21, 21)

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
        ENV_HV1Y2 | P35961: 1g9n 1rzk 1yyl 1yym 2i5y 2i60 2ny7 2qad 3hi1 3tgq 4dvr 4jo3 4jzw 4jzz 4k0a 4laj 4r4f 4rqs 4rwy 5a7x 5a8h

(-) Related Entries Specified in the PDB File

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2i60 CRYSTAL STRUCTURE OF [PHE23]M47, A SCORPION-TOXIC MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B
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