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(-) Description

Title :  STRUCTURE OF THE GP41 N-TRIMER IN COMPLEX WITH THE HIV ENTRY INHIBITOR PIE7
 
Authors :  A. P. Vandemark, B. Welch, A. Heroux, C. P. Hill, M. S. Kay
Date :  03 Sep 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A,B,C,H,K,L
Keywords :  Hiv, Viral Entry, Pie, 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, C
    Engineered: YES
    Other Details: PEPTIDE SYNTHESIS
    Synthetic: YES
 
Molecule 2 - HIV ENTRY INHIBITOR PIE7
    Chains: H, K, L
    Engineered: YES
    Other Details: PEPTIDE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCHKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (15, 57)

Asymmetric/Biological Unit (15, 57)
No.NameCountTypeFull Name
1ACE6Mod. Amino AcidACETYL GROUP
2DAL9Mod. Amino AcidD-ALANINE
3DAS3Mod. Amino AcidD-ASPARTIC ACID
4DCY6Mod. Amino AcidD-CYSTEINE
5DGL3Mod. Amino AcidD-GLUTAMIC ACID
6DGN3Mod. Amino AcidD-GLUTAMINE
7DLE3Mod. Amino AcidD-LEUCINE
8DLY3Mod. Amino AcidD-LYSINE
9DPR3Mod. Amino AcidD-PROLINE
10DTR6Mod. Amino AcidD-TRYPTOPHAN
11DTY3Mod. Amino AcidD-TYROSINE
12EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
13GOL1Ligand/IonGLYCEROL
14NH26Mod. Amino AcidAMINO GROUP
15SO41Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDLY H:1 , GLY H:2 , DAS H:5 , DTY H:6 , HOH H:42BINDING SITE FOR RESIDUE ACE H 0
02AC2SOFTWAREDLE H:12 , DCY H:13 , DAL H:14 , DAL H:15 , HOH H:34BINDING SITE FOR RESIDUE NH2 H 16
03AC3SOFTWAREDLY K:1 , GLY K:2BINDING SITE FOR RESIDUE ACE K 0
04AC4SOFTWARELEU B:32 , HOH B:470 , DLE K:12 , DCY K:13 , DAL K:14 , DAL K:15BINDING SITE FOR RESIDUE NH2 K 16
05AC5SOFTWAREGLU B:6 , GLU B:10 , EPE B:430 , DLY L:1BINDING SITE FOR RESIDUE ACE L 0
06AC6SOFTWARELEU C:32 , DLE L:12 , DCY L:13 , DAL L:14 , DAL L:15 , HOH L:25BINDING SITE FOR RESIDUE NH2 L 16
07AC7SOFTWARELYS A:27 , ARG B:25 , HOH B:457 , HOH B:468 , HOH K:17BINDING SITE FOR RESIDUE SO4 B 47
08AC8SOFTWAREALA A:42 , ARG A:43 , LEU A:45 , NH2 A:46 , ACE B:0 , ARG B:1 , MET B:2 , LYS B:3 , GLU B:6 , HOH B:436 , HOH B:469 , ARG C:1 , ACE L:0 , DLY L:1BINDING SITE FOR RESIDUE EPE B 430
09AC9SOFTWARELEU A:40 , ARG A:43 , ILE A:44 , HOH A:74 , GLN C:41 , ILE C:44 , LEU C:45 , HOH H:17BINDING SITE FOR RESIDUE GOL A 47
10BC1SOFTWARELEU A:29 , LEU A:32 , TRP A:35 , GLY A:36 , GLN A:39 , ILE C:37 , LYS C:38 , GLN C:41 , ACE H:0 , NH2 H:16 , HOH H:17 , HOH H:18 , HOH H:19 , HOH H:20 , HOH H:21 , HOH H:22 , HOH H:24 , HOH H:25 , HOH H:27 , HOH H:28 , HOH H:30 , HOH H:33 , HOH H:35 , HOH H:38BINDING SITE FOR CHAIN H OF HIV ENTRY INHIBITOR PIE7
11BC2SOFTWAREVAL A:34 , LYS A:38 , GLN A:41 , LEU B:32 , TRP B:35 , LEU B:40 , HOH B:455 , GLU C:20 , ASN C:21 , ALA C:24 , HOH C:62 , HOH C:75 , HOH C:83 , ACE K:0 , NH2 K:16 , HOH K:17 , HOH K:18 , HOH K:19 , HOH K:20 , HOH K:21 , HOH K:22 , HOH K:23 , HOH K:25 , HOH K:29 , HOH K:31BINDING SITE FOR CHAIN K OF HIV ENTRY INHIBITOR PIE7
12BC3SOFTWAREVAL B:34 , LYS B:38 , GLN B:41 , EPE B:430 , LEU C:29 , LEU C:32 , TRP C:35 , ACE L:0 , NH2 L:16 , HOH L:17 , HOH L:18 , HOH L:19 , HOH L:20 , HOH L:21 , HOH L:22 , HOH L:23 , HOH L:24 , HOH L:28 , HOH L:29 , HOH L:30 , HOH L:31BINDING SITE FOR CHAIN L OF HIV ENTRY INHIBITOR PIE7

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1H:4 -H:13
2K:4 -K:13
3L:4 -L:13

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R5D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R5D)

(-) Exons   (0, 0)

(no "Exon" information available for 2R5D)

(-) 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:47
                                                                              
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains -2r5dA00 A:1-45                               - CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2r5d A  0 xRMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARILx 46
                            |        9        19        29        39      |
                            |                                            46-NH2
                            0-ACE                                          


Chain B from PDB  Type:PROTEIN  Length:47
                                                                              
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains -2r5dB00 B:1-45                               - CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2r5d B  0 xRMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARILx 46
                            |        9        19        29        39      |
                            |                                            46-NH2
                            0-ACE                                          


Chain C from PDB  Type:PROTEIN  Length:47
                                                                              
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains -2r5dC00 C:1-45                               - CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2r5d C  0 xRMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARILx 46
                            |        9        19        29        39      |
                            |                                            46-NH2
                            0-ACE                                          


Chain H from PDB  Type:PROTEIN  Length:17
                                                
               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
                  2r5d H  0 xxGxxxxxxxxxxxxxx 16
                            || ||||||9|||||||
                            || ||||||9-DTR|||
                            0-ACE||||10-DGN||
                             1-DLY||| 11-DTR|
                               3-DAL|  12-DLE
                                4-DCY   13-DCY
                                 5-DAS   14-DAL
                                  6-DTY   15-DAL
                                   7-DPR   16-NH2
                                    8-DGL    


Chain K from PDB  Type:PROTEIN  Length:17
                                                
               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
                  2r5d K  0 xxGxxxxxxxxxxxxxx 16
                            || ||||||9|||||||
                            || ||||||9-DTR|||
                            0-ACE||||10-DGN||
                             1-DLY||| 11-DTR|
                               3-DAL|  12-DLE
                                4-DCY   13-DCY
                                 5-DAS   14-DAL
                                  6-DTY   15-DAL
                                   7-DPR   16-NH2
                                    8-DGL    


Chain L from PDB  Type:PROTEIN  Length:17
                                                
               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
                  2r5d L  0 xxGxxxxxxxxxxxxxx 16
                            || ||||||9|||||||
                            || ||||||9-DTR|||
                            0-ACE||||10-DGN||
                             1-DLY||| 11-DTR|
                               3-DAL|  12-DLE
                                4-DCY   13-DCY
                                 5-DAS   14-DAL
                                  6-DTY   15-DAL
                                   7-DPR   16-NH2
                                    8-DGL
   Legend:   → Mismatch (orange background)
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    → 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 2R5D)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R5D)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2R5D)

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2r3c 2r5b