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(-) Description

Title :  GRAMICIDIN D FROM BACILLUS BREVIS (ACTIVE FORM)
 
Authors :  B. M. Burkhart, W. A. Pangborn, W. L. Duax
Date :  11 May 98  (Deposition) - 14 Oct 98  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gramicidin, Antifungal, Antibacterial, Antibiotic, Membrane Ion Channel, Linear Gramicidin, Double Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Burkhart, N. Li, D. A. Langs, W. A. Pangborn, W. L. Duax
The Conducting Form Of Gramicidin A Is A Right-Handed Double-Stranded Double Helix.
Proc. Natl. Acad. Sci. Usa V. 95 12950 1998
PubMed-ID: 9789021  |  Reference-DOI: 10.1073/PNAS.95.22.12950

(-) Compounds

Molecule 1 - GRAMICIDIN A
    Chains: A, B
    Organism Scientific: BREVIBACILLUS BREVIS
    Organism Taxid: 1393
    Synonym: VALYL GRAMICIDIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1ACY5Ligand/IonACETIC ACID
2DLE8Mod. Amino AcidD-LEUCINE
3DVA4Mod. Amino AcidD-VALINE
4ETA2Mod. Amino AcidETHANOLAMINE
5FVA2Mod. Amino AcidN-FORMYL-L-VALINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDLE A:4 , ALA A:5 , ETA A:16 , ETA B:16BINDING SITE FOR RESIDUE ACY A 201
2AC2SOFTWARETRP A:15BINDING SITE FOR RESIDUE ACY A 205
3AC3SOFTWAREDLE B:4 , ALA B:5 , ACY B:203BINDING SITE FOR RESIDUE ACY B 202
4AC4SOFTWARETRP A:11 , ALA B:5 , DVA B:6 , TRP B:11 , ACY B:202BINDING SITE FOR RESIDUE ACY B 203
5AC5SOFTWARETRP B:15 , ETA B:16BINDING SITE FOR RESIDUE ACY B 206
6AC6SOFTWAREACY A:201 , ACY A:205 , HOH A:2005 , HOH A:2006 , HOH A:2010 , HOH A:2011 , HOH A:2013 , 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 , ACY B:203 , ACY B:206BINDING SITE FOR CHAIN A OF GRAMICIDIN A
7AC7SOFTWAREGLY 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 , ACY A:201 , HOH A:2011 , ACY B:202 , ACY B:203 , ACY B:206 , HOH B:2006BINDING SITE FOR CHAIN B OF GRAMICIDIN A

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BDW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BDW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BDW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BDW)

(-) Exons   (0, 0)

(no "Exon" information available for 1BDW)

(-) 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    
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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 d1bdwa_ A:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1bdw 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 d1bdwb_ B:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1bdw B  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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1BDW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BDW)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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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

1al4 CRYSTAL STRUCTURE OF GRAMICIDIN D IN N-PROPANOL
1alx CRYSTAL STRUCTURE OF GRAMICIDIN D IN METHANOL
1alz CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL
1av2 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE
1c4d CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE
1gmk CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLRXED WITH POTASSIUM THIOCYANATE
1grm SOLUTION STRUCTURE OF THE GRAMICIDIN A
1jno SOLUTION STRUCTURE OF GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES
1jo3 SOLUTION STRUCTURE OF GRAMICIDIN B IN SODIUM DODECYL SULFATE MICELLES
1jo4 SOLUTION STRUCTURE OF GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES
1kqe SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A IN BENZENE/ACETONE 10:1
1mag SOLID STATE NMR STRUCTURE OF GRAMICIDIN A IN HYDRATED DMPC BILAYERS,
1mic SOLUTION STRUCTURE OF GRAMICIDIN A IN METHANOL IN THE PRESENCE OF CACL
1ng8 SOLUTION STRUCTURE OF GRAMICIDIN A (W15G) IN SODIUM DODECYL SULFATE MICELLES
1nrm SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES
1nru SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES IN THE PRESENCE OF EXCESS NA+
1nt5 SOLUTION STRUCTURE OF GRAMICIDIN A (V1F) IN SODIUM DODECYL SULFATE MICELLES
1nt6 SOLUTION STRUCTURE OF F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES
1tk2 CRYSTAL STRUCTURE OF GRAMICIDIN S COMPLEXED WITH ALKALINE PROTEINASE SAVINASE
1tkq SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN A IN A MEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE, IN THE PRESENCE OF CSCL
1w5u CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL
2izq CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH KI IN METHANOL
2xdc CRYSTAL STRUCTURE OF GRAMICIDIN A FROM CRYSTALS GROWN IN A LIPID CUBIC PHASE.
3l8l CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH NAI