Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  GRAMICIDIN/KSCN COMPLEX
 
Authors :  D. A. Doyle, B. A. Wallace
Date :  09 Jul 96  (Deposition) - 01 Jul 98  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Gramicidin, Antifungal, Antibacterial, Antibiotic, Membrane Ion Channel, Linear Gramicidin, Double Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Doyle, B. A. Wallace
Crystal Structure Of The Gramicidin/Potassium Thiocyanate Complex.
J. Mol. Biol. V. 266 963 1997
PubMed-ID: 9086274  |  Reference-DOI: 10.1006/JMBI.1996.0837
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 65)

Asymmetric Unit (7, 65)
No.NameCountTypeFull Name
1DLE16Mod. Amino AcidD-LEUCINE
2DVA8Mod. Amino AcidD-VALINE
3ETA4Mod. Amino AcidETHANOLAMINE
4FVA4Mod. Amino AcidN-FORMYL-L-VALINE
5K4Ligand/IonPOTASSIUM ION
6MOH25Ligand/IonMETHANOL
7SCN4Ligand/IonTHIOCYANATE ION
Biological Unit 1 (6, 31)
No.NameCountTypeFull Name
1DLE8Mod. Amino AcidD-LEUCINE
2DVA4Mod. Amino AcidD-VALINE
3ETA2Mod. Amino AcidETHANOLAMINE
4FVA2Mod. Amino AcidN-FORMYL-L-VALINE
5K-1Ligand/IonPOTASSIUM ION
6MOH14Ligand/IonMETHANOL
7SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (6, 30)
No.NameCountTypeFull Name
1DLE8Mod. Amino AcidD-LEUCINE
2DVA4Mod. Amino AcidD-VALINE
3ETA2Mod. Amino AcidETHANOLAMINE
4FVA2Mod. Amino AcidN-FORMYL-L-VALINE
5K-1Ligand/IonPOTASSIUM ION
6MOH11Ligand/IonMETHANOL
7SCN3Ligand/IonTHIOCYANATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:13 , DLE A:14 , TRP A:15 , ETA A:16BINDING SITE FOR RESIDUE K A 17
02AC2SOFTWAREDLE A:4 , ALA A:5 , TRP B:11 , DLE B:12 , DLE B:14BINDING SITE FOR RESIDUE SCN A 18
03AC3SOFTWAREDLE A:10 , TRP A:11BINDING SITE FOR RESIDUE SCN A 19
04AC4SOFTWARETRP A:9 , DLE A:10 , DVA B:6 , VAL B:7 , DVA B:8BINDING SITE FOR RESIDUE K B 17
05AC5SOFTWAREGLY A:2BINDING SITE FOR RESIDUE SCN B 18
06AC6SOFTWAREETA C:16BINDING SITE FOR RESIDUE K C 17
07AC7SOFTWAREALA C:3 , DLE C:4 , ALA C:5 , DVA C:6 , TRP D:9 , TRP D:11 , DLE D:12 , DLE D:14BINDING SITE FOR RESIDUE SCN C 18
08AC8SOFTWARETRP C:9 , TRP C:11 , ALA D:5 , DVA D:6 , VAL D:7 , DVA D:8BINDING SITE FOR RESIDUE K D 17
09AC9SOFTWAREK A:17 , SCN A:18 , SCN A:19 , 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 , K B:17 , SCN B:18 , DLE C:4 , VAL C:7 , TRP C:11 , DLE C:12 , DLE C:14 , TRP C:15 , TRP D:9 , DLE D:10 , TRP D:11 , TRP D:15BINDING SITE FOR CHAIN A OF GRAMICIDIN A
10BC1SOFTWAREGLY 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 , K A:17 , SCN A:18 , K B:17 , SCN B:18 , DVA C:6 , VAL C:7 , TRP C:11 , DLE C:12 , TRP C:15 , DLE D:4 , DVA D:6 , TRP D:9 , DLE D:10 , TRP D:11 , TRP D:13 , DLE D:14 , TRP D:15BINDING SITE FOR CHAIN B OF GRAMICIDIN A
11BC2SOFTWAREDLE A:4 , VAL A:7 , TRP A:11 , TRP A:13 , DLE B:4 , TRP B:9 , TRP B:11 , TRP B:13 , K C:17 , SCN C:18 , 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 , K D:17BINDING SITE FOR CHAIN C OF GRAMICIDIN A
12BC3SOFTWAREDLE A:4 , DVA A:6 , TRP A:9 , TRP A:11 , DLE B:4 , DVA B:6 , DVA B:8 , TRP B:9 , DLE B:10 , TRP B:11 , TRP B:13 , DLE B:14 , 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 , K C:17 , SCN C:18 , K D:17BINDING SITE FOR CHAIN D OF GRAMICIDIN A

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GMK)

(-) 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 d1gmka_ A:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1gmk 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 d1gmkb_ B:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1gmk 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 d1gmkc_ C:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1gmk 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 d1gmkd_ D:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .ee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1gmk D  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

Asymmetric Unit
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1GMK)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    DLE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DVA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ETA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FVA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MOH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SCN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1gmk)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1gmk
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1GMK)

(-) 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
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