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(-) Description

Title :  STRUCTURE OF THE GP41 N-PEPTIDE IN COMPLEX WITH THE HIV ENTRY INHIBITOR PIE1
 
Authors :  A. P. Vandemark, B. Welch, A. Heroux, C. P. Hill, M. S. Kay
Date :  29 Aug 07  (Deposition) - 02 Oct 07  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (3x)
Biol. Unit 2:  B,C  (3x)
Keywords :  Hiv, Inhibitor, Viral Entry, Pie, Viral Protein, Viral Protein-Viral Protein Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Welch, A. P. Vandemark, A. Heroux, C. P. Hill, M. S. Kay
Potent D-Peptide Inhibitors Of Hiv-1 Entry
Proc. Natl. Acad. Sci. Usa V. 104 16828 2007
PubMed-ID: 17942675  |  Reference-DOI: 10.1073/PNAS.0708109104

(-) Compounds

Molecule 1 - GP41 N-PEPTIDE
    Chains: A, B
    Engineered: YES
    Other Details: PEPTIDE SYNTHESIS
    Synthetic: YES
 
Molecule 2 - HIV ENTRY INHIBITOR PIE1
    Chains: C, D
    Engineered: YES
    Other Details: PEPTIDE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): A  D
Biological Unit 2 (3x): ABC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (13, 38)

Asymmetric Unit (13, 38)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CL1Ligand/IonCHLORIDE ION
3DAL6Mod. Amino AcidD-ALANINE
4DCY4Mod. Amino AcidD-CYSTEINE
5DGL4Mod. Amino AcidD-GLUTAMIC ACID
6DGN2Mod. Amino AcidD-GLUTAMINE
7DLE2Mod. Amino AcidD-LEUCINE
8DLY1Mod. Amino AcidD-LYSINE
9DPR2Mod. Amino AcidD-PROLINE
10DSN2Mod. Amino AcidD-SERINE
11DTR4Mod. Amino AcidD-TRYPTOPHAN
12NH24Mod. Amino AcidAMINO GROUP
13YT35Ligand/IonYTTRIUM (III) ION
Biological Unit 1 (12, 57)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2CL-1Ligand/IonCHLORIDE ION
3DAL9Mod. Amino AcidD-ALANINE
4DCY6Mod. Amino AcidD-CYSTEINE
5DGL6Mod. Amino AcidD-GLUTAMIC ACID
6DGN3Mod. Amino AcidD-GLUTAMINE
7DLE3Mod. Amino AcidD-LEUCINE
8DLY3Mod. Amino AcidD-LYSINE
9DPR3Mod. Amino AcidD-PROLINE
10DSN3Mod. Amino AcidD-SERINE
11DTR6Mod. Amino AcidD-TRYPTOPHAN
12NH26Mod. Amino AcidAMINO GROUP
13YT36Ligand/IonYTTRIUM (III) ION
Biological Unit 2 (10, 54)
No.NameCountTypeFull Name
1ACE-1Mod. Amino AcidACETYL GROUP
2CL-1Ligand/IonCHLORIDE ION
3DAL9Mod. Amino AcidD-ALANINE
4DCY6Mod. Amino AcidD-CYSTEINE
5DGL6Mod. Amino AcidD-GLUTAMIC ACID
6DGN3Mod. Amino AcidD-GLUTAMINE
7DLE3Mod. Amino AcidD-LEUCINE
8DLY-1Mod. Amino AcidD-LYSINE
9DPR3Mod. Amino AcidD-PROLINE
10DSN3Mod. Amino AcidD-SERINE
11DTR6Mod. Amino AcidD-TRYPTOPHAN
12NH26Mod. Amino AcidAMINO GROUP
13YT39Ligand/IonYTTRIUM (III) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , GLU A:10 , HOH A:635 , DGL C:9 , HOH C:24 , HOH C:30BINDING SITE FOR RESIDUE YT3 A 501
2AC2SOFTWAREGLN A:16BINDING SITE FOR RESIDUE YT3 A 503
3AC3SOFTWARETHR A:33BINDING SITE FOR RESIDUE CL A 601
4AC4SOFTWAREASP B:7 , GLU B:10 , HOH B:510 , HOH B:526 , DGL D:9 , HOH D:29BINDING SITE FOR RESIDUE YT3 B 502
5AC5SOFTWAREGLN B:16BINDING SITE FOR RESIDUE YT3 B 504
6AC6SOFTWARELEU B:30 , THR B:33BINDING SITE FOR RESIDUE YT3 B 505
7AC7SOFTWAREGLU A:10 , GLU A:13 , SER A:14 , LYS A:17 , ASN A:21 , YT3 A:501 , HOH A:632 , LEU B:29 , LEU B:32 , VAL B:34 , TRP B:35 , GLY B:36 , LYS B:38 , GLN B:41 , LEU B:45 , HOH B:538 , HOH C:20 , HOH C:22 , HOH C:23 , HOH C:24 , HOH C:25 , HOH C:27 , HOH C:29 , HOH C:30 , HOH C:36 , HOH C:37 , HOH C:38BINDING SITE FOR CHAIN C OF HIV ENTRY INHIBITOR PIE1
8AC8SOFTWARELEU A:29 , LEU A:32 , VAL A:34 , TRP A:35 , GLY A:36 , ILE A:37 , LYS A:38 , GLN A:41 , HOH A:688 , GLU B:10 , GLU B:13 , SER B:14 , LYS B:17 , ASN B:21 , YT3 B:502 , HOH B:555 , HOH D:18 , HOH D:19 , HOH D:20 , HOH D:21 , HOH D:22 , HOH D:25 , HOH D:26 , HOH D:28 , HOH D:29 , HOH D:30 , HOH D:32 , HOH D:33 , HOH D:34 , HOH D:35 , HOH D:36 , HOH D:37 , HOH D:38BINDING SITE FOR CHAIN D OF HIV ENTRY INHIBITOR PIE1

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:5 -C:14
2D:5 -D:14

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R3C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R3C)

(-) Exons   (0, 0)

(no "Exon" information available for 2R3C)

(-) Sequences/Alignments

Asymmetric 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:47
                                                                              
               SCOP domains -d2r3ca1 A:1-45                               - SCOP domains
               CATH domains -2r3cA00 A:1-45                               - CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2r3c A  0 xRMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARILx 46
                            |        9        19        29        39      |
                            |                                            46-NH2
                            0-ACE                                          


Chain B from PDB  Type:PROTEIN  Length:43
                                                                          
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains 2r3cB00 B:4-45                            - CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                  2r3c B  4 QIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARILx 46
                                    13        23        33        43  |
                                                                     46-NH2


Chain C from PDB  Type:PROTEIN  Length:15
                                              
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhh..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                  2r3c C  3 Gxxxxxxxxxxxxxx 17
                             |||||||12|||||
                             |||||||12-DTR|
                             4-DAL|||13-DLE
                              5-DCY|| 14-DCY
                               6-DGL|  15-DAL
                                7-DSN   16-DAL
                                 8-DPR   17-NH2
                                  9-DGL    
                                  10-DTR   
                                   11-DGN  


Chain D from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2r3c D  2 xGxxxxxxxxxxxxxx 17
                            | ||||||11||||||
                            | ||||||11-DGN||
                            2-DLY||||12-DTR|
                              4-DAL|| 13-DLE
                               5-DCY|  14-DCY
                                6-DGL   15-DAL
                                 7-DSN   16-DAL
                                  8-DPR   17-NH2
                                   9-DGL    
                                   10-DTR
   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  (1, 1)

Asymmetric Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R3C)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2R3C)

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2r5b 2r5d