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(-) Description

Title :  GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
 
Authors :  B. M. Burkhart, W. A. Pangborn, W. L. Duax, D. A. Langs
Date :  06 Jun 97  (Deposition) - 04 Mar 98  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gramicidin, Antifungal, Antibiotic, Antibacterial, Membrane Ion Channel, Linear Gramicidin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Burkhart, R. M. Gassman, D. A. Langs, W. A. Pangborn, W. L. Duax
Heterodimer Formation And Crystal Nucleation Of Gramicidin
Biophys. J. V. 75 2135 1998
PubMed-ID: 9788907  |  Reference-DOI: 10.1016/S0006-3495(98)77656-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ILE-GRAMICIDIN C
    Chains: A
    Organism Scientific: BREVIBACILLUS BREVIS
    Organism Taxid: 1393
 
Molecule 2 - VAL-GRAMICIDIN A
    Chains: B
    Organism Scientific: BREVIBACILLUS BREVIS
    Organism Taxid: 1393

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 31)

Asymmetric/Biological Unit (6, 31)
No.NameCountTypeFull Name
1DLE8Mod. Amino AcidD-LEUCINE
2DVA4Mod. Amino AcidD-VALINE
3EOH14Ligand/IonETHANOL
4ETA2Mod. Amino AcidETHANOLAMINE
5FVA2Mod. Amino AcidN-FORMYL-L-VALINE
6QIL1Mod. Amino AcidN-FORMYL-L-ISOLEUCINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:2 , EOH A:510 , EOH A:511 , EOH A:512 , DLE B:10BINDING SITE FOR RESIDUE EOH A 501
02AC2SOFTWAREDLE A:4 , EOH A:513 , EOH A:514 , TRP B:9 , TRP B:13 , TRP B:15 , ETA B:16 , EOH B:506BINDING SITE FOR RESIDUE EOH A 504
03AC3SOFTWARETRP A:9 , TRP A:15 , ETA A:16 , EOH A:509 , EOH A:513 , TRP B:13BINDING SITE FOR RESIDUE EOH A 505
04AC4SOFTWAREDLE A:4 , TRP A:9 , DLE A:10 , DLE A:12 , EOH A:510BINDING SITE FOR RESIDUE EOH A 507
05AC5SOFTWAREVAL A:7 , DVA A:8 , TRP A:9 , TRP A:15 , EOH A:505 , DLE B:12BINDING SITE FOR RESIDUE EOH A 509
06AC6SOFTWARETRP A:13 , EOH A:501 , EOH A:507 , EOH A:511BINDING SITE FOR RESIDUE EOH A 510
07AC7SOFTWARETRP A:13 , DLE A:14 , EOH A:501 , EOH A:510 , EOH A:512 , HOH A:2001 , GLY B:2 , DLE B:10BINDING SITE FOR RESIDUE EOH A 511
08AC8SOFTWAREGLY A:2 , EOH A:501 , EOH A:511 , EOH A:514BINDING SITE FOR RESIDUE EOH A 512
09AC9SOFTWAREETA A:16 , EOH A:504 , EOH A:505 , EOH A:514 , TRP B:13 , ETA B:16BINDING SITE FOR RESIDUE EOH A 513
10BC1SOFTWAREALA A:5 , VAL A:7 , DVA A:8 , EOH A:504 , EOH A:512 , EOH A:513 , TRP B:9 , TRP B:11 , TRP B:13 , EOH B:506 , EOH B:508BINDING SITE FOR RESIDUE EOH A 514
11BC2SOFTWARETRP A:15 , ETA A:16 , DLE B:4 , EOH B:508BINDING SITE FOR RESIDUE EOH B 502
12BC3SOFTWAREETA A:16 , HOH A:2001 , TRP B:15BINDING SITE FOR RESIDUE EOH B 503
13BC4SOFTWARETYR A:11 , ETA A:16 , EOH A:504 , EOH A:514 , TRP B:9 , DLE B:10 , EOH B:508BINDING SITE FOR RESIDUE EOH B 506
14BC5SOFTWAREEOH A:514 , TRP B:13 , EOH B:502 , EOH B:506BINDING SITE FOR RESIDUE EOH B 508
15BC6SOFTWAREEOH A:501 , EOH A:504 , EOH A:505 , EOH A:507 , EOH A:509 , EOH A:510 , EOH A:511 , EOH A:512 , EOH A:513 , EOH A:514 , HOH A:2001 , 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 , EOH B:502 , EOH B:503 , EOH B:506BINDING SITE FOR CHAIN A OF ILE-GRAMICIDIN C
16BC7SOFTWAREGLY 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 , TYR A:11 , DLE A:12 , TRP A:13 , DLE A:14 , TRP A:15 , ETA A:16 , EOH A:501 , EOH A:504 , EOH A:505 , EOH A:507 , EOH A:509 , EOH A:511 , EOH A:512 , EOH A:513 , EOH A:514 , EOH B:502 , EOH B:503 , EOH B:506 , EOH B:508BINDING SITE FOR CHAIN B OF VAL-GRAMICIDIN A

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ALZ)

(-) 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 d1alza_ 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
                  1alz A  1 xGAxAxVxWxYWxWxWx 16
                            |  | | |10  | | |
                            |  | | | |  | | |
                            1-QIL| | |  | | |
                               4-DLE |  | | |
                                 6-DVA  | | |
                                   8-DVA| | |
                                    10-DLE| |
                                       12-DLE
                                         14-DLE
                                           16-ETA


Chain B from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains d1alzb_ B:       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
                  1alz B  1 xGAxAxVxWxWxWxWx 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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  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 1ALZ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
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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
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
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