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(-) Description

Title :  GRAMICIDIN D COMPLEX WITH KI
 
Authors :  A. Olczak, M. L. Glowka, M. Szczesio, J. Bojarska, W. L. Duax, B. M. Burkh Z. Wawrzak
Date :  26 Jul 06  (Deposition) - 23 Jan 07  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Antibiotic, Gramicidin, Antifungal, Antibacterial, Membrane Ion Channel, Linear Gramicidin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Olczak, M. L. Glowka, M. Szczesio, J. Bojarska, W. L. Duax, B. M. Burkhart, Z. Wawrzak
Nonstoichiometric Complex Of Gramicidin D With Ki At 0. 80 A Resolution.
Acta Crystallogr. , Sect. D V. 63 319 2007
PubMed-ID: 17327669  |  Reference-DOI: 10.1107/S0907444906053649

(-) Compounds

Molecule 1 - GRAMICIDIN D
    Chains: A, B, C, D
    Organism Scientific: BREVIBACILLUS BREVIS
    Organism Taxid: 1393
    Other Details: SIGMA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (7, 53)
No.NameCountTypeFull Name
1DLE16Mod. Amino AcidD-LEUCINE
2DVA8Mod. Amino AcidD-VALINE
3ETA4Mod. Amino AcidETHANOLAMINE
4FVA4Mod. Amino AcidN-FORMYL-L-VALINE
5IOD8Ligand/IonIODIDE ION
6K6Ligand/IonPOTASSIUM ION
7MOH7Ligand/IonMETHANOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDVA A:6 , VAL A:7 , DVA A:8 , HOH A:2011 , HOH A:2012 , HOH A:2013 , HOH A:2018 , HOH A:2020 , DVA B:8 , DLE B:10 , HOH B:2009 , HOH B:2011BINDING SITE FOR RESIDUE K A1016
02AC2SOFTWAREFVA A:1 , GLY A:2 , HOH A:2001 , HOH A:2002 , HOH A:2003 , HOH A:2004 , HOH A:2005 , HOH A:2008 , HOH A:2030 , DLE B:14 , ETA B:16BINDING SITE FOR RESIDUE K A1017
03AC3SOFTWARETRP A:9 , IOD A:1020 , TRP B:15 , HOH B:2012 , HOH B:2014 , HOH D:2015BINDING SITE FOR RESIDUE IOD A1018
04AC4SOFTWARETRP A:9 , IOD A:1020 , TRP B:15 , HOH B:2012 , HOH B:2014 , HOH D:2015BINDING SITE FOR RESIDUE IOD A1019
05AC5SOFTWAREIOD A:1018 , IOD A:1019 , TRP B:13 , TRP B:15 , HOH B:2012 , HOH B:2013 , HOH B:2014 , TRP C:9 , TRP D:15BINDING SITE FOR RESIDUE IOD A1020
06AC6SOFTWARETRP A:13 , DLE A:14 , TRP A:15 , IOD A:1022 , HOH A:2010 , HOH A:2023 , HOH A:2024BINDING SITE FOR RESIDUE IOD A1021
07AC7SOFTWAREDLE A:12 , TRP A:13 , IOD A:1021 , HOH A:2010 , HOH A:2024 , TRP C:11 , DLE D:4BINDING SITE FOR RESIDUE IOD A1022
08AC8SOFTWARETYR A:11 , ETA A:16 , HOH A:2017 , HOH A:2019 , HOH A:2021 , TRP C:13 , TRP C:15 , HOH C:2016 , HOH C:2017BINDING SITE FOR RESIDUE IOD A1023
09AC9SOFTWAREDLE A:10 , PHE A:11 , DLE A:12 , HOH A:2015 , HOH A:2016 , HOH A:2022 , HOH A:2026 , DLE B:4 , ALA B:5 , DVA B:6 , VAL B:7 , HOH B:2006BINDING SITE FOR RESIDUE K B1016
10BC1SOFTWAREDVA C:6 , DVA C:8 , K C:1017 , HOH C:2010 , HOH C:2013 , DVA D:8 , TRP D:9 , DLE D:10 , HOH D:2008 , HOH D:2010BINDING SITE FOR RESIDUE K C1016
11BC2SOFTWAREDVA C:6 , TRP C:9 , K C:1016 , HOH C:2006 , HOH C:2007 , HOH C:2009 , DLE D:10 , TRP D:13 , HOH D:2008BINDING SITE FOR RESIDUE K C1017
12BC3SOFTWAREDLE C:14 , HOH C:2015 , HOH C:2018 , HOH C:2019 , FVA D:1 , GLY D:2 , ALA D:3 , HOH D:2002 , HOH D:2003 , HOH D:2006BINDING SITE FOR RESIDUE K D1016
13BC4SOFTWAREDLE A:4 , DLE B:12 , TRP D:11 , HOH D:2011BINDING SITE FOR RESIDUE IOD D1017
14BC5SOFTWARETRP A:9 , HOH A:2006 , HOH A:2014 , TRP D:9BINDING SITE FOR RESIDUE IOD D1018
15BC6SOFTWAREK A:1016 , K A:1017 , IOD A:1018 , IOD A:1019 , IOD A:1021 , IOD A:1022 , IOD A:1023 , HOH A:2002 , HOH A:2003 , HOH A:2005 , HOH A:2006 , HOH A:2007 , HOH A:2008 , HOH A:2011 , HOH A:2012 , HOH A:2013 , HOH A:2014 , HOH A:2015 , HOH A:2016 , HOH A:2017 , HOH A:2018 , HOH A:2019 , HOH A:2020 , HOH A:2022 , HOH A:2024 , HOH A:2026 , HOH A:2027 , HOH A:2029 , 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 , TYR B:11 , TRP B:11 , DLE B:12 , TRP B:13 , DLE B:14 , TRP B:15 , ETA B:16 , K B:1016 , HOH B:2001 , HOH B:2010 , HOH B:2013 , FVA C:1 , DVA C:6 , VAL C:7 , TRP C:9 , TRP C:11 , PHE C:11 , TYR C:11 , DLE C:12 , TRP C:13 , DLE C:14 , TRP C:15 , HOH C:2017 , FVA D:1 , DLE D:4 , DVA D:6 , VAL D:7 , TRP D:11 , TRP D:13 , TRP D:15 , ETA D:16 , IOD D:1017 , IOD D:1018BINDING SITE FOR CHAIN A OF GRAMICIDIN D
16BC7SOFTWAREFVA 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 , TYR A:11 , PHE A:11 , DLE A:12 , TRP A:13 , DLE A:14 , TRP A:15 , ETA A:16 , K A:1016 , K A:1017 , IOD A:1018 , IOD A:1019 , IOD A:1020 , HOH A:2002 , HOH A:2006 , HOH A:2010 , HOH A:2013 , HOH A:2026 , HOH A:2029 , K B:1016 , HOH B:2001 , HOH B:2002 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2007 , HOH B:2009 , HOH B:2010 , HOH B:2011 , HOH B:2012 , HOH B:2014 , HOH B:2015 , HOH B:2016 , DLE C:4 , DVA C:6 , VAL C:7 , DVA C:8 , TRP C:9 , DLE C:10 , TRP C:11 , PHE C:11 , TYR C:11 , TRP C:13 , TRP C:15 , ETA C:16 , HOH C:2001 , ALA D:3 , DLE D:4 , TRP D:9 , TYR D:11 , TRP D:11 , DLE D:12 , TRP D:13 , DLE D:14 , TRP D:15 , ETA D:16 , IOD D:1017 , HOH D:2011 , HOH D:2012 , HOH D:2013BINDING SITE FOR CHAIN B OF GRAMICIDIN D
17BC8SOFTWAREFVA A:1 , DVA A:6 , VAL A:7 , TRP A:9 , TRP A:11 , PHE A:11 , TYR A:11 , DLE A:12 , TRP A:13 , DLE A:14 , TRP A:15 , ETA A:16 , IOD A:1020 , IOD A:1022 , IOD A:1023 , HOH A:2014 , FVA B:1 , DVA B:6 , VAL B:7 , TRP B:9 , TRP B:11 , TYR B:11 , TRP B:13 , DLE B:14 , ETA B:16 , K C:1016 , K C:1017 , HOH C:2002 , HOH C:2003 , HOH C:2005 , HOH C:2006 , HOH C:2007 , HOH C:2008 , HOH C:2010 , HOH C:2011 , HOH C:2012 , HOH C:2013 , HOH C:2014 , HOH C:2016 , HOH C:2017 , HOH C:2019 , HOH C:2020 , 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 , K D:1016 , HOH D:2008 , HOH D:2010 , HOH D:2015BINDING SITE FOR CHAIN C OF GRAMICIDIN D
18BC9SOFTWAREFVA A:1 , DLE A:4 , DVA A:6 , VAL A:7 , TRP A:9 , TYR A:11 , TRP A:11 , PHE A:11 , DLE A:12 , TRP A:13 , TRP A:15 , IOD A:1020 , IOD A:1022 , HOH A:2010 , HOH A:2023 , DLE B:4 , TRP B:9 , TRP B:11 , TYR B:11 , DLE B:12 , TRP B:13 , DLE B:14 , TRP B:15 , ETA B:16 , 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 , PHE C:11 , TRP C:11 , TYR C:11 , DLE C:12 , TRP C:13 , DLE C:14 , TRP C:15 , ETA C:16 , K C:1016 , K C:1017 , HOH C:2006 , HOH C:2010 , HOH C:2019 , K D:1016 , IOD D:1017 , IOD D:1018 , HOH D:2001 , HOH D:2002 , HOH D:2004 , HOH D:2005 , HOH D:2007 , HOH D:2008 , HOH D:2010BINDING SITE FOR CHAIN D OF GRAMICIDIN D

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IZQ)

(-) 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    
   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: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
                  2izq A  1 xGAxAxVxWxWYxWxWx 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 .ee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                  2izq 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: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
                  2izq C  1 xGAxAxVxWxWYxWxWx 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 .ee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                  2izq D  1 xGAxAxVxWxWYxWxWx 16
                            |  | | |10  | | |
                            |  | | | |  | | |
                            1-FVA| | |  | | |
                               4-DLE |  | | |
                                 6-DVA  | | |
                                   8-DVA| | |
                                    10-DLE| |
                                       12-DLE
                                         14-DLE
                                           16-ETA
   Legend:   → Mismatch (orange background)
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IZQ)

(-) 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
1w5u CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL
2xdc CRYSTAL STRUCTURE OF GRAMICIDIN A FROM CRYSTALS GROWN IN A LIPID CUBIC PHASE.
3l8l CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH NAI