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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 :  2.00
Chains :  Asym. Unit :  A,B,C,H,K,L
Biol. Unit 1:  A,B,C,H,K,L  (1x)
Biol. Unit 2:  A,B,C,H,K,L  (2x)
Biol. Unit 3:  A,B,C,H,K,L  (2x)
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 Unit : ABCHKL
Biological Unit 1 (1x): ABCHKL
Biological Unit 2 (2x): ABCHKL
Biological Unit 3 (2x): ABCHKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (13, 56)

Asymmetric Unit (13, 56)
No.NameCountTypeFull Name
1ACE5Mod. 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
12NH26Mod. Amino AcidAMINO GROUP
13SO43Ligand/IonSULFATE ION
Biological Unit 1 (13, 56)
No.NameCountTypeFull Name
1ACE5Mod. 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
12NH26Mod. Amino AcidAMINO GROUP
13SO43Ligand/IonSULFATE ION
Biological Unit 2 (13, 112)
No.NameCountTypeFull Name
1ACE10Mod. Amino AcidACETYL GROUP
2DAL18Mod. Amino AcidD-ALANINE
3DAS6Mod. Amino AcidD-ASPARTIC ACID
4DCY12Mod. Amino AcidD-CYSTEINE
5DGL6Mod. Amino AcidD-GLUTAMIC ACID
6DGN6Mod. Amino AcidD-GLUTAMINE
7DLE6Mod. Amino AcidD-LEUCINE
8DLY6Mod. Amino AcidD-LYSINE
9DPR6Mod. Amino AcidD-PROLINE
10DTR12Mod. Amino AcidD-TRYPTOPHAN
11DTY6Mod. Amino AcidD-TYROSINE
12NH212Mod. Amino AcidAMINO GROUP
13SO46Ligand/IonSULFATE ION
Biological Unit 3 (13, 112)
No.NameCountTypeFull Name
1ACE10Mod. Amino AcidACETYL GROUP
2DAL18Mod. Amino AcidD-ALANINE
3DAS6Mod. Amino AcidD-ASPARTIC ACID
4DCY12Mod. Amino AcidD-CYSTEINE
5DGL6Mod. Amino AcidD-GLUTAMIC ACID
6DGN6Mod. Amino AcidD-GLUTAMINE
7DLE6Mod. Amino AcidD-LEUCINE
8DLY6Mod. Amino AcidD-LYSINE
9DPR6Mod. Amino AcidD-PROLINE
10DTR12Mod. Amino AcidD-TRYPTOPHAN
11DTY6Mod. Amino AcidD-TYROSINE
12NH212Mod. Amino AcidAMINO GROUP
13SO46Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:32 , DLE H:12 , DCY H:13 , DAL H:14 , DAL H:15BINDING SITE FOR RESIDUE NH2 H 16
02AC2SOFTWARELEU C:32 , DLY K:1 , GLY K:2 , GLY L:2 , DAL L:3 , DCY L:4BINDING SITE FOR RESIDUE ACE K 0
03AC3SOFTWARELEU B:29 , DLE K:12 , DCY K:13 , DAL K:14 , DAL K:15 , HOH K:32BINDING SITE FOR RESIDUE NH2 K 16
04AC4SOFTWARELEU B:32 , TRP B:35 , GLY K:2 , DAL K:3 , HOH K:17 , DLY L:1BINDING SITE FOR RESIDUE ACE L 0
05AC5SOFTWARELEU C:32 , DLE L:12 , DCY L:13 , DAL L:14 , DAL L:15 , HOH L:20BINDING SITE FOR RESIDUE NH2 L 16
06AC6SOFTWAREGLN B:31 , HOH B:57 , HOH B:74 , TRP C:35 , LYS C:38 , GLN C:39 , HOH C:67 , DLY L:1 , HOH L:22BINDING SITE FOR RESIDUE SO4 B 47
07AC7SOFTWARELYS B:28 , ACE C:0 , ARG C:1 , DLY L:1BINDING SITE FOR RESIDUE SO4 B 48
08AC8SOFTWAREACE A:0 , ARG A:1 , MET A:2 , LYS A:3 , GLN A:4BINDING SITE FOR RESIDUE SO4 A 47
09AC9SOFTWARELEU A:32 , TRP A:35 , GLY A:36 , LEU A:40 , ARG A:43 , GLN B:4 , VAL C:34 , ILE C:37 , LYS C:38 , GLN C:41 , HOH C:53 , NH2 H:16 , HOH H:18 , HOH H:21 , HOH H:22 , HOH H:23 , HOH H:24 , HOH H:27 , HOH H:28 , DGN L:10 , DTR L:11 , DAL L:14BINDING SITE FOR CHAIN H OF HIV ENTRY INHIBITOR PIE7
10BC1SOFTWAREVAL A:34 , LYS A:38 , GLN A:41 , NH2 A:46 , LYS B:3 , LEU B:29 , LEU B:32 , TRP B:35 , HOH B:53 , ARG C:1 , 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:24 , HOH K:25 , HOH K:26 , HOH K:28 , HOH K:29 , HOH K:30 , HOH K:34 , ACE L:0 , DAS L:5BINDING SITE FOR CHAIN K OF HIV ENTRY INHIBITOR PIE7
11BC2SOFTWAREACE B:0 , ARG B:1 , MET B:2 , LYS B:38 , GLN B:41 , SO4 B:47 , SO4 B:48 , HOH B:51 , HOH B:53 , HOH B:57 , HOH B:75 , ARG C:1 , LEU C:32 , TRP C:35 , DTR H:11 , DAL H:14 , HOH H:25 , ACE K:0 , GLY K:2 , DAS K:5 , ACE L:0 , NH2 L:16 , HOH L:17 , HOH L:18 , HOH L:19 , HOH L:21 , HOH L:22 , HOH L:23 , HOH L:24 , HOH L:25 , HOH L:26 , HOH L:27 , HOH L:30BINDING SITE FOR CHAIN L OF HIV ENTRY INHIBITOR PIE7

(-) SS Bonds  (3, 3)

Asymmetric 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 2R5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R5B)

(-) Exons   (0, 0)

(no "Exon" information available for 2R5B)

(-) 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 ----------------------------------------------- SCOP domains
               CATH domains -2r5bA00 A:1-45                               - CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2r5b 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 -2r5bB00 B:1-45                               - CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2r5b 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 -2r5bC00 C:1-45                               - CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  2r5b C  0 xRMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARILx 46
                            |        9        19        29        39      |
                            |                                            46-NH2
                            0-ACE                                          


Chain H 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
                  2r5b H  1 xGxxxxxxxxxxxxxx 16
                            | ||||||10||||||
                            | ||||||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    
                                    9-DTR   


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
                  2r5b 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
                  2r5b 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
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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 '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2R5B)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R5B)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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2r3c 2r5d