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(-) Description

Title :  CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U7 IN COMPLEX WITH HIV-1 YU2 GP120
 
Authors :  P. Acharya, P. D. Kwong
Date :  03 Apr 13  (Deposition) - 12 Jun 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym./Biol. Unit :  A,R
Keywords :  Hiv-1 Attachment Glycoprotein Gp120, Hiv-1 Envelope, Viral Protein- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Acharya, T. S. Luongo, M. K. Louder, K. Mckee, Y. Yang, Y. Do Kwon, J. R. Mascola, P. Kessler, L. Martin, P. D. Kwong
Structural Basis For Highly Effective Hiv-1 Neutralization By Cd4-Mimetic Miniproteins Revealed By 1. 5 A Cocrystal Structure Of Gp120 And M48U1.
Structure V. 21 1018 2013
PubMed-ID: 23707685  |  Reference-DOI: 10.1016/J.STR.2013.04.015

(-) Compounds

Molecule 1 - HIV-1 YU2 GP120 GLYCOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: GP120
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: YU2
 
Molecule 2 - CD4-MIMETIC MINIPROTEIN M48U7
    Chains: R
    Engineered: YES
    Other Details: M48U7 IS A SYNTHETIC MINIPROTEIN 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  (7, 17)

Asymmetric/Biological Unit (7, 17)
No.NameCountTypeFull Name
11OP1Mod. Amino AcidO-(5-HYDROXYPENTYL)-L-TYROSINE
2DPR1Mod. Amino AcidD-PROLINE
3FLC1Ligand/IonCITRATE ANION
4IPA4Ligand/IonISOPROPYL ALCOHOL
5MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:44 , TRP A:45 , GLU A:91BINDING SITE FOR RESIDUE IPA A 509
02AC2SOFTWAREGLN A:246BINDING SITE FOR RESIDUE IPA A 510
03AC3SOFTWAREALA A:73 , VAL A:120 , ILE A:423 , LYS A:432 , MET A:434BINDING SITE FOR RESIDUE IPA A 511
04AC4SOFTWARETRP A:96 , LYS A:97 , ASN A:98 , VAL A:101 , ARG A:480BINDING SITE FOR RESIDUE IPA A 512
05AC5SOFTWARESER A:110 , GLN A:114 , ARG A:419 , LYS A:421 , GLN A:422 , ILE A:423 , HOH A:711BINDING SITE FOR RESIDUE FLC A 513
06AC6SOFTWAREASN A:234 , THR A:236 , SER A:274 , HOH A:683BINDING SITE FOR MONO-SACCHARIDE NAG A 502 BOUND TO ASN A 234
07AC7SOFTWARELYS A:231 , ASN A:241BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 241
08AC8SOFTWAREGLU A:211 , LEU A:261 , ASN A:262 , CYS A:445 , SER A:446 , SER A:447 , HOH A:607 , HOH A:611 , HOH A:649BINDING SITE FOR MONO-SACCHARIDE NAG A 504 BOUND TO ASN A 262
09AC9SOFTWARELYS A:46 , ASN A:92 , ASN A:276 , THR A:278 , ASN A:279 , HOH A:682BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 276
10BC1SOFTWAREGLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLU A:290 , LYS A:348 , GLU A:351 , HOH A:669 , HOH A:701BINDING SITE FOR MONO-SACCHARIDE NAG A 505 BOUND TO ASN A 289
11BC2SOFTWAREASN A:295 , ASN A:332 , LEU A:333 , ASN A:413 , ARG A:444 , HOH A:742BINDING SITE FOR MONO-SACCHARIDE NAG A 506 BOUND TO ASN A 295
12BC3SOFTWAREASN A:386 , THR A:388 , HOH A:736BINDING SITE FOR MONO-SACCHARIDE NAG A 507 BOUND TO ASN A 386
13BC4SOFTWARESER A:291 , ASN A:448 , HOH A:615 , HOH A:651BINDING SITE FOR MONO-SACCHARIDE NAG A 508 BOUND TO ASN A 448
14BC5SOFTWARETHR A:63 , LYS A:207 , VAL A:255 , THR A:257 , ALA A:281 , SER A:365 , GLY A:366 , GLY A:367 , ASP A:368 , GLU A:370 , SER A:375 , PHE A:382 , TYR A:384 , ASN A:425 , MET A:426 , TRP A:427 , GLU A:429 , ARG A:440 , GLY A:473 , HOH A:605 , HOH A:614 , HOH A:643 , HOH A:681 , HOH R:101 , HOH R:102 , HOH R:103 , HOH R:104BINDING SITE FOR CHAIN R OF CD4-MIMETIC MINIPROTEIN M48U7

(-) SS Bonds  (10, 10)

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:1 -R:19
9R:6 -R:24
10R:10 -R:26

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K0A)

(-) Exons   (0, 0)

(no "Exon" information available for 4K0A)

(-) 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..hhhhhee....eeeeeeeee.eee......eee........eeeeeeeeeeeeee......eeeeee....hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k0a A  44 VWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKNGTEIFRPGGGDMRDNWRSELYKYKVVKIE 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 329       339       349       359       369       379       389      |413       423       433       443       453      |465       475       485       
                                                                                                          124|                                                                                                    301|                                                                    396|                                              460|                             
                                                                                                           198                                                                                                     325                                                                     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 .hhhhhhhhhhhhh.eeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 4k0a R   1 xNLHFCQLRCKSLGLLGRCAxTyCACVx  28
                            |       10        20| |    |
                            1-MPT              21-DPR  |
                                                 23-1OP|
                                                      28-NH2
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4K0A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K0A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K0A)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        ENV_HV1Y2 | P35961: 1g9n 1rzk 1yyl 1yym 2i5y 2i60 2ny7 2qad 3hi1 3tgq 4dvr 4jo3 4jzw 4jzz 4ka2 4laj 4r4f 4rqs 4rwy 5a7x 5a8h

(-) Related Entries Specified in the PDB File

4jzw 'CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U1 IN COMPLEX WITH HIV-1 YU2 GP120 IN P212121 SPACE GROUP
4jzz 'CRYSTAL STRUCTURE OF CD4-MIMETIC MINIPROTEIN M48U1 IN COMPLEX WITH HIV-1 YU2 GP120 IN C2221 SPACE GROUP
4k0a