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(-) Description

Title :  CRYSTAL STRUCTURE OF LIPOPEPTIDE DETERGENT (LPD-12)
 
Authors :  D. N. Ho, N. C. Pomroy, J. A. Cuesta-Seijo, G. G. Prive
Date :  20 Feb 08  (Deposition) - 09 Sep 08  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F,G,H  (1x)
Biol. Unit 2:  I,J,K,L  (2x)
Keywords :  Alpha Helix, Acyl Chains, Detergent, Amphiphilic, Lipopeptide, Self-Assembling Peptide, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. N. Ho, N. C. Pomroy, J. A. Cuesta-Seijo, G. G. Prive
Crystal Structure Of A Self-Assembling Lipopeptide Detergent At 1. 20 A.
Proc. Natl. Acad. Sci. Usa V. 105 12861 2008
PubMed-ID: 18753631  |  Reference-DOI: 10.1073/PNAS.0801941105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LPD-12
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    Engineered: YES
    Other Details: DE NOVO DESIGNED LIPOPEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCDEFGH    
Biological Unit 2 (2x):         IJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 70)

Asymmetric Unit (4, 70)
No.NameCountTypeFull Name
1ACE12Mod. Amino AcidACETYL GROUP
2LMT22Ligand/IonDODECYL-BETA-D-MALTOSIDE
3NH212Mod. Amino AcidAMINO GROUP
4O1224Mod. Amino AcidN~5~-DODECANOYL-L-ORNITHINE
Biological Unit 1 (4, 44)
No.NameCountTypeFull Name
1ACE8Mod. Amino AcidACETYL GROUP
2LMT12Ligand/IonDODECYL-BETA-D-MALTOSIDE
3NH28Mod. Amino AcidAMINO GROUP
4O1216Mod. Amino AcidN~5~-DODECANOYL-L-ORNITHINE
Biological Unit 2 (4, 52)
No.NameCountTypeFull Name
1ACE8Mod. Amino AcidACETYL GROUP
2LMT20Ligand/IonDODECYL-BETA-D-MALTOSIDE
3NH28Mod. Amino AcidAMINO GROUP
4O1216Mod. Amino AcidN~5~-DODECANOYL-L-ORNITHINE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01FC4SOFTWAREALA A:9 , LYS H:8 , LYS H:11 , GLU H:15 , HOH H:509 , HOH H:511 , HOH H:521 , HOH H:522 , HOH H:525 , HOH H:526 , HOH H:529 , HOH H:544 , HOH K:544 , LYS L:11 , GLU L:15BINDING SITE FOR RESIDUE LMT H 501
02FC5SOFTWAREALA B:20 , HOH B:240BINDING SITE FOR RESIDUE LMT B 502
03FC6SOFTWAREALA B:16 , LYS C:8 , ALA C:9 , TYR C:12 , HOH C:521 , HOH C:533BINDING SITE FOR RESIDUE LMT C 503
04FC7SOFTWAREALA A:10 , LYS B:8 , ALA B:9 , ALA B:10 , TYR B:12 , HOH B:342 , HOH B:343 , TYR C:12BINDING SITE FOR RESIDUE LMT B 504
05FC8SOFTWAREALA C:20BINDING SITE FOR RESIDUE LMT C 505
06GC1SOFTWAREALA E:9 , TYR E:12BINDING SITE FOR RESIDUE LMT E 507
07GC2SOFTWARETYR F:12 , LYS G:8 , ALA G:9 , TYR G:12 , HOH G:67 , HOH G:402BINDING SITE FOR RESIDUE LMT G 508
08GC3SOFTWAREALA F:5 , LYS F:8 , HOH F:525BINDING SITE FOR RESIDUE LMT F 509
09GC4SOFTWARETYR F:12 , ALA G:10BINDING SITE FOR RESIDUE LMT G 510
10GC5SOFTWAREALA H:10BINDING SITE FOR RESIDUE LMT C 511
11GC6SOFTWARELYS A:8 , LYS A:11 , GLU A:15 , HOH A:514 , HOH A:524 , HOH A:526 , HOH A:530 , HOH A:532 , HOH A:534 , HOH A:548 , LYS E:11 , GLU E:15 , HOH E:508BINDING SITE FOR RESIDUE LMT A 512
12GC8SOFTWARETYR I:12 , ALA L:1 , ALA L:5BINDING SITE FOR RESIDUE LMT I 514
13GC9SOFTWAREGLU I:4 , ALA I:5 , LYS I:8 , HOH I:517 , HOH I:547 , LYS L:8 , ALA L:9 , TYR L:12BINDING SITE FOR RESIDUE LMT I 515
14HC1SOFTWAREALA J:9 , TYR J:12 , TYR K:12BINDING SITE FOR RESIDUE LMT J 516
15HC2SOFTWARETYR J:12 , ALA K:9 , TYR K:12BINDING SITE FOR RESIDUE LMT K 517
16HC3SOFTWAREALA C:25 , HOH I:523BINDING SITE FOR RESIDUE LMT K 518
17HC5SOFTWARETYR K:12BINDING SITE FOR RESIDUE LMT K 520
18HC6SOFTWAREHOH I:546 , ALA K:6 , ALA L:16 , LYS L:19 , ALA L:20 , HOH L:535BINDING SITE FOR RESIDUE LMT L 521
19HC7SOFTWAREALA I:23 , HOH L:547BINDING SITE FOR RESIDUE LMT L 522

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CAY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CAY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CAY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CAY)

(-) Exons   (0, 0)

(no "Exon" information available for 3CAY)

(-) 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:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay A  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain B from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay B  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain C from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay C  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain D from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay D  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain E from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay E  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain F from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay F  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain G from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay G  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain H from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay H  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain I from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay I  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain J from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay J  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain K from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay K  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12                    


Chain L from PDB  Type:PROTEIN  Length:27
                                                          
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3cay L  0 xAxAEAAEKAAKYAAEAAEKAAKAxAx 26
                            | |      9        19    | |
                            | |                    24-O12
                            0-ACE                    26-NH2
                              2-O12
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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3cba