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(-) Description

Title :  STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A LIPID CUBIC PHASE.
 
Authors :  N. Hoefer, D. Aragao, M. Caffrey
Date :  30 Apr 10  (Deposition) - 11 Aug 10  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  E,F  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Antibiotic, Ion Channel, Monoolein, Lipid Cubic Phase, Mesophase Sponge Phase, Bilayer, Antifungal, Antibacterial (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Hoefer, D. Aragao, M. Caffrey
Crystallizing Transmembrane Peptides In Lipidic Mesophases
Biophys. J. V. 99 23 2010
PubMed-ID: 20682243  |  Reference-DOI: 10.1016/J.BPJ.2010.05.011

(-) Compounds

Molecule 1 - GRAMICIDIN A
    Atcc: 8246
    Chains: A, B, C, D, E, F
    Organism Scientific: BREVIBACILLUS BREVIS
    Organism Taxid: 1393
    Synonym: VALYL GRAMICIDIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):     EF
Biological Unit 3 (1x):   CD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 53)

Asymmetric Unit (6, 53)
No.NameCountTypeFull Name
115P4Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2DLE24Mod. Amino AcidD-LEUCINE
3DVA12Mod. Amino AcidD-VALINE
4ETA6Mod. Amino AcidETHANOLAMINE
5FVA6Mod. Amino AcidN-FORMYL-L-VALINE
6NA1Ligand/IonSODIUM ION
Biological Unit 1 (5, 19)
No.NameCountTypeFull Name
115P3Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2DLE8Mod. Amino AcidD-LEUCINE
3DVA4Mod. Amino AcidD-VALINE
4ETA2Mod. Amino AcidETHANOLAMINE
5FVA2Mod. Amino AcidN-FORMYL-L-VALINE
6NA-1Ligand/IonSODIUM ION
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2DLE8Mod. Amino AcidD-LEUCINE
3DVA4Mod. Amino AcidD-VALINE
4ETA2Mod. Amino AcidETHANOLAMINE
5FVA2Mod. Amino AcidN-FORMYL-L-VALINE
6NA-1Ligand/IonSODIUM ION
Biological Unit 3 (5, 17)
No.NameCountTypeFull Name
115P1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2DLE8Mod. Amino AcidD-LEUCINE
3DVA4Mod. Amino AcidD-VALINE
4ETA2Mod. Amino AcidETHANOLAMINE
5FVA2Mod. Amino AcidN-FORMYL-L-VALINE
6NA-1Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:15 , ETA A:16 , 15P A:1017 , NA A:1018 , DLE B:4 , DLE C:4 , TRP D:15 , ETA D:16 , DLE E:14 , TRP E:15BINDING SITE FOR RESIDUE 15P A1016
02AC2SOFTWARE15P A:1016 , NA A:1018 , FVA B:1 , TRP D:15 , ETA D:16BINDING SITE FOR RESIDUE 15P A1017
03AC3SOFTWARE15P A:1016 , 15P A:1017 , TRP D:15BINDING SITE FOR RESIDUE NA A1018
04AC4SOFTWARETRP A:9 , DLE A:10 , TRP A:11 , TRP B:9 , DLE B:10 , TRP B:11 , TRP C:9 , TRP C:13 , 15P C:1016 , DLE D:10 , TRP D:11 , TRP D:15 , TRP E:9 , TRP E:13 , DLE F:10 , TRP F:11 , TRP F:15BINDING SITE FOR RESIDUE 15P B1016
05AC5SOFTWARE15P B:1016 , DVA C:8 , TRP C:13BINDING SITE FOR RESIDUE 15P C1016
06AC6SOFTWARE15P A:1016 , FVA B:1 , GLY B:2 , ALA B:3 , DLE B:4 , ALA B:5 , DVA B:6 , VAL B:7 , DVA B:8 , TRP B:9 , DLE B:10 , TRP B:11 , DLE B:12 , TRP B:13 , DLE B:14 , TRP B:15 , ETA B:16 , 15P B:1016 , ALA C:5 , TRP C:13 , GLY D:2 , ALA E:5 , ALA F:3 , DVA F:8BINDING SITE FOR CHAIN A OF GRAMICIDIN A
07AC7SOFTWAREFVA A:1 , GLY A:2 , ALA A:3 , DLE A:4 , ALA A:5 , DVA A:6 , VAL A:7 , DVA A:8 , TRP A:9 , DLE A:10 , TRP A:11 , DLE A:12 , TRP A:13 , DLE A:14 , TRP A:15 , ETA A:16 , 15P A:1016 , 15P A:1017 , 15P B:1016 , ALA C:5 , ALA D:3 , DVA D:8 , ALA E:5 , TRP E:13 , GLY F:2 , TRP F:11BINDING SITE FOR CHAIN B OF GRAMICIDIN A
08AC8SOFTWAREALA A:3 , TRP A:11 , 15P A:1016 , DLE B:4 , 15P B:1016 , 15P C:1016 , FVA D:1 , GLY D:2 , ALA D:3 , DLE D:4 , ALA D:5 , DVA D:6 , VAL D:7 , DVA D:8 , TRP D:9 , DLE D:10 , TRP D:11 , DLE D:12 , TRP D:13 , DLE D:14 , TRP D:15 , ETA D:16 , TRP F:11BINDING SITE FOR CHAIN C OF GRAMICIDIN A
09AC9SOFTWAREGLY A:2 , 15P A:1016 , 15P A:1017 , NA A:1018 , DLE B:12 , TRP B:13 , 15P B:1016 , GLY C:2 , ALA C:3 , DLE C:4 , ALA C:5 , DVA C:6 , VAL C:7 , DVA C:8 , TRP C:9 , DLE C:10 , TRP C:11 , DLE C:12 , TRP C:13 , DLE C:14 , TRP C:15 , ETA C:16 , TRP E:9BINDING SITE FOR CHAIN D OF GRAMICIDIN A
10BC1SOFTWAREDLE A:4 , 15P A:1016 , ALA B:3 , TRP B:11 , 15P B:1016 , TRP D:11 , HOH E:2001 , HOH E:2002 , FVA F:1 , ALA F:3 , DLE F:4 , ALA F:5 , DVA F:6 , VAL F:7 , DVA F:8 , TRP F:9 , DLE F:10 , TRP F:11 , DLE F:12 , TRP F:13 , DLE F:14 , TRP F:15 , ETA F:16BINDING SITE FOR CHAIN E OF GRAMICIDIN A
11BC2SOFTWAREDLE A:12 , TRP A:13 , GLY B:2 , TRP B:11 , 15P B:1016 , TRP C:9 , GLY E:2 , ALA E:3 , DLE E:4 , ALA E:5 , DVA E:6 , VAL E:7 , DVA E:8 , TRP E:9 , DLE E:10 , TRP E:11 , DLE E:12 , TRP E:13 , DLE E:14 , TRP E:15 , ETA E:16 , HOH E:2001BINDING SITE FOR CHAIN F OF GRAMICIDIN A

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XDC)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XDC)

(-) 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:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2xdc A  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain B from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2xdc B  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain C from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2xdc C  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain D from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2xdc D  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain E from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2xdc E  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain F from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2xdc F  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA
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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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(-) Pfam Domains  (0, 0)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

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