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(-) Description

Title :  GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
 
Authors :  M. L. Glowka, A. Olczak, J. Bojarska, M. Szczesio, W. L. Duax, B. M. Burkh W. A. Pangborn, D. A. Langs, Z. Wawrzak
Date :  10 Aug 04  (Deposition) - 15 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.14
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibiotic, Gramicidin, Antifungal, Antibacterial, Membrane Ion Channel, Linear Gramicidin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Glowka, A. Olczak, J. Bojarska, M. Szczesio, W. L. Duax, B. M. Burkhart, W. A. Pangborn, D. A. Langs, Z. Wawrzak
Structure Of Gramicidin D-Rbcl Complex At Atomic Resolution From Low-Temperature Synchrotron Data: Interactions Of Double-Stranded Gramicidin Channel Contents And Cations With Channel Wall
Acta Crystallogr. , Sect. D V. 61 433 2005
PubMed-ID: 15805598  |  Reference-DOI: 10.1107/S0907444905000399

(-) Compounds

Molecule 1 - GRAMICIDIN D
    Chains: A, C
    Organism Scientific: BACILLUS BREVIS
    Organism Taxid: 1393
    Synonym: VAL-GRAMICIDIN A
 
Molecule 2 - GRAMICIDIN D
    Chains: B, D
    Organism Scientific: BACILLUS BREVIS
    Organism Taxid: 1393
    Synonym: VAL-GRAMICIDIN A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 53)

Asymmetric Unit (7, 53)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2DLE16Mod. Amino Acid
3DVA8Mod. Amino AcidD-VALINE
4EOH1Ligand/IonETHANOL
5ETA4Mod. Amino AcidETHANOLAMINE
6FVA4Mod. Amino AcidN-FORMYL-L-VALINE
7RB14Ligand/IonRUBIDIUM ION
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DLE8Mod. Amino Acid
3DVA4Mod. Amino AcidD-VALINE
4EOH-1Ligand/IonETHANOL
5ETA2Mod. Amino AcidETHANOLAMINE
6FVA2Mod. Amino AcidN-FORMYL-L-VALINE
7RB-1Ligand/IonRUBIDIUM ION
Biological Unit 2 (5, 17)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DLE8Mod. Amino Acid
3DVA4Mod. Amino AcidD-VALINE
4EOH1Ligand/IonETHANOL
5ETA2Mod. Amino AcidETHANOLAMINE
6FVA2Mod. Amino AcidN-FORMYL-L-VALINE
7RB-1Ligand/IonRUBIDIUM ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:2 , DLE A:4 , ALA A:5 , RB A:1018 , HOH A:2002 , HOH A:2004 , DLE B:12 , TRP B:15 , RB C:1021BINDING SITE FOR RESIDUE RB A1017
02AC2SOFTWAREGLY A:2 , ALA A:5 , RB A:1017 , HOH A:2004 , DLE B:14 , TRP B:15 , ETA B:16 , RB C:1021BINDING SITE FOR RESIDUE RB A1018
03AC3SOFTWARETRP A:13 , TRP A:15 , HOH A:2007 , VAL B:7 , TRP B:9 , TRP C:13 , TRP C:15 , TRP D:9BINDING SITE FOR RESIDUE CL A1019
04AC4SOFTWARETRP A:15 , ETA A:16 , TRP C:9BINDING SITE FOR RESIDUE CL A1020
05AC5SOFTWAREDLE A:14 , ETA A:16 , GLY B:2 , RB C:1016BINDING SITE FOR RESIDUE RB B1016
06AC6SOFTWAREDVA A:8 , DLE A:10 , HOH A:2005 , DVA B:6 , VAL B:7 , DVA B:8 , RB B:1018 , HOH B:2002 , HOH B:2003 , HOH B:2005BINDING SITE FOR RESIDUE RB B1017
07AC7SOFTWAREDVA A:8 , DLE A:10 , DVA B:8 , TRP B:11 , RB B:1017 , HOH B:2004 , HOH B:2005 , HOH B:2008BINDING SITE FOR RESIDUE RB B1018
08AC8SOFTWAREDLE A:4 , TYR B:11 , TRP B:11 , CL B:1020 , HOH B:2006 , TRP C:9 , TRP D:13 , DLE D:14 , TRP D:15BINDING SITE FOR RESIDUE CL B1019
09AC9SOFTWARETRP B:9 , CL B:1019 , HOH B:2006 , TRP D:15BINDING SITE FOR RESIDUE CL B1020
10BC1SOFTWAREFVA B:1 , TRP B:13BINDING SITE FOR RESIDUE CL B1021
11BC2SOFTWAREDLE A:12 , DLE A:14 , HOH A:2006 , GLY B:2 , DLE B:4 , RB B:1016 , HOH B:2002BINDING SITE FOR RESIDUE RB C1016
12BC3SOFTWARETRP A:9 , DLE C:4 , ALA C:5 , RB C:1022 , ETA D:16BINDING SITE FOR RESIDUE EOH C1017
13BC4SOFTWAREDLE C:14 , TRP C:15 , ETA C:16 , FVA D:1 , GLY D:2 , ALA D:5 , RB D:1016 , HOH D:2006BINDING SITE FOR RESIDUE RB C1018
14BC5SOFTWAREDVA C:6 , VAL C:7 , RB C:1020 , RB C:1022 , TRP D:13 , DLE D:14 , TRP D:15 , HOH D:2004 , HOH D:2009 , HOH D:2010 , HOH D:2011BINDING SITE FOR RESIDUE RB C1019
15BC6SOFTWAREGLY C:2 , DLE C:4 , ALA C:5 , RB C:1019 , RB C:1022 , DLE D:14 , HOH D:2010 , HOH D:2011BINDING SITE FOR RESIDUE RB C1020
16BC7SOFTWAREDLE A:4 , ALA A:5 , VAL A:7 , RB A:1017 , RB A:1018 , HOH A:2002 , DLE B:12 , DLE B:14 , TRP B:15 , HOH B:2007BINDING SITE FOR RESIDUE RB C1021
17BC8SOFTWAREGLY C:2 , ALA C:5 , EOH C:1017 , RB C:1019 , RB C:1020 , DLE D:14 , TRP D:15 , ETA D:16 , HOH D:2010BINDING SITE FOR RESIDUE RB C1022
18BC9SOFTWAREDLE C:12 , DLE C:14 , RB C:1018 , HOH C:2003 , GLY D:2 , DLE D:4 , HOH D:2002BINDING SITE FOR RESIDUE RB D1016
19CC1SOFTWAREDVA C:8 , DLE C:10 , HOH C:2001 , DVA D:6 , VAL D:7 , DVA D:8 , RB D:1018 , HOH D:2002 , HOH D:2008BINDING SITE FOR RESIDUE RB D1017
20CC2SOFTWAREDVA C:8 , DLE C:10 , DVA D:8 , DLE D:10 , RB D:1017 , HOH D:2004 , HOH D:2007BINDING SITE FOR RESIDUE RB D1018
21CC3SOFTWAREDLE A:10 , DLE B:12 , TRP B:13 , DLE B:14 , TRP B:15 , DLE C:4 , TRP D:11 , TYR D:11BINDING SITE FOR RESIDUE CL D1019
22CC4SOFTWARERB A:1017 , RB A:1018 , CL A:1019 , CL A:1020 , HOH A:2003 , HOH A:2004 , HOH A:2005 , HOH A:2007 , 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 , TYR B:11 , DLE B:12 , TRP B:13 , DLE B:14 , TRP B:15 , ETA B:16 , RB B:1016 , RB B:1017 , RB B:1018 , CL B:1019 , DLE C:4 , TRP C:9 , TRP C:11 , DLE C:12 , TRP C:13 , DLE C:14 , TRP C:15 , ETA C:16 , RB C:1016 , EOH C:1017 , RB C:1021 , DVA D:6 , DVA D:8 , TRP D:9 , DLE D:10 , TRP D:11 , TYR D:11 , TRP D:13 , TRP D:15 , CL D:1019BINDING SITE FOR CHAIN A OF GRAMICIDIN D
23CC5SOFTWAREFVA 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 , RB A:1017 , RB A:1018 , CL A:1019 , RB B:1016 , RB B:1017 , RB B:1018 , CL B:1019 , CL B:1020 , CL B:1021 , HOH B:2001 , HOH B:2004 , HOH B:2007 , FVA C:1 , DVA C:6 , VAL C:7 , TRP C:9 , TRP C:11 , TRP C:15 , ETA C:16 , RB C:1016 , RB C:1021 , FVA D:1 , DVA D:6 , TRP D:9 , TRP D:11 , TYR D:11 , DLE D:12 , TRP D:13 , DLE D:14 , TRP D:15 , CL D:1019BINDING SITE FOR CHAIN B OF GRAMICIDIN D
24CC6SOFTWARETRP A:9 , TRP A:11 , TRP A:13 , DLE A:14 , TRP A:15 , ETA A:16 , CL A:1019 , CL A:1020 , HOH A:2008 , DLE B:4 , DVA B:6 , VAL B:7 , TRP B:11 , TYR B:11 , TRP B:13 , TRP B:15 , ETA B:16 , CL B:1019 , HOH B:2006 , EOH C:1017 , RB C:1018 , RB C:1019 , RB C:1020 , RB C:1022 , HOH C:2001 , HOH C:2002 , 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 , TYR D:11 , TRP D:11 , DLE D:12 , TRP D:13 , DLE D:14 , TRP D:15 , ETA D:16 , RB D:1016 , RB D:1017 , RB D:1018 , CL D:1019 , HOH D:2003BINDING SITE FOR CHAIN C OF GRAMICIDIN D
25CC7SOFTWAREFVA A:1 , DVA A:6 , VAL A:7 , TRP A:11 , TRP A:13 , DLE A:14 , ETA A:16 , CL A:1019 , FVA B:1 , DVA B:6 , TRP B:9 , DLE B:10 , TYR B:11 , TRP B:11 , DLE B:12 , TRP B:13 , DLE B:14 , TRP B:15 , CL B:1019 , CL B:1020 , FVA C:1 , 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 , EOH C:1017 , RB C:1018 , RB C:1019 , RB C:1020 , RB C:1022 , RB D:1016 , RB D:1017 , RB D:1018 , CL D:1019 , HOH D:2003 , HOH D:2006 , HOH D:2009BINDING SITE FOR CHAIN D OF GRAMICIDIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W5U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W5U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W5U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W5U)

(-) Exons   (0, 0)

(no "Exon" information available for 1W5U)

(-) 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 .eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1w5u 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:17
                                                
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                  1w5u B  1 xGAxAxVxWxWYxWxWx 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 .eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1w5u 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:17
                                                
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                  1w5u D  1 xGAxAxVxWxWYxWxWx 16
                            |  | | |10  | | |
                            |  | | | |  | | |
                            1-FVA| | |  | | |
                               4-DLE |  | | |
                                 6-DVA  | | |
                                   8-DVA| | |
                                    10-DLE| |
                                       12-DLE
                                         14-DLE
                                           16-ETA
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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (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

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
1bdw CRYSTAL STRUCTURE OF GRAMICIDIN A FROM BACILLUS BREVIS
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
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