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(-) Description

Title :  STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 7.7 MONOACYLGLYCEROL LIPID CUBIC PHASE.
 
Authors :  N. Hoefer, D. Aragao, M. Caffrey
Date :  14 Jan 11  (Deposition) - 11 May 11  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.08
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Antibiotic, Ion Channel, Mesophase, Sponge Phase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Hoefer, D. Aragao, J. Lyons, M. Caffrey
Membrane Protein Crystallization In Lipidic Mesophases. Hosting Lipid Effects On The Crystallization And Structure Of A Transmembrane Peptide
Cryst. Growth Des. V. 11 1182 2011
PubMed-ID: 22933857  |  Reference-DOI: 10.1021/CG101384P

(-) Compounds

Molecule 1 - VAL-GRAMICIDIN A
    Atcc: 8246
    Chains: A, B, C, D, E, F
    Organism Scientific: BREVIBACILLUS BREVIS
    Organism Taxid: 1393
    Synonym: GRAMICIDIN D

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 51)

Asymmetric Unit (5, 51)
No.NameCountTypeFull Name
115P3Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2DLE24Mod. Amino AcidD-LEUCINE
3DVA12Mod. Amino AcidD-VALINE
4ETA6Mod. Amino AcidETHANOLAMINE
5FVA6Mod. Amino AcidN-FORMYL-L-VALINE
Biological Unit 1 (5, 19)
No.NameCountTypeFull Name
115P3Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2DLE8Mod. Amino AcidD-LEUCINE
3DVA4Mod. Amino AcidD-VALINE
4ETA2Mod. Amino AcidETHANOLAMINE
5FVA2Mod. Amino AcidN-FORMYL-L-VALINE
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2DLE8Mod. Amino AcidD-LEUCINE
3DVA4Mod. Amino AcidD-VALINE
4ETA2Mod. Amino AcidETHANOLAMINE
5FVA2Mod. Amino AcidN-FORMYL-L-VALINE
Biological Unit 3 (4, 16)
No.NameCountTypeFull Name
115P-1Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2DLE8Mod. Amino AcidD-LEUCINE
3DVA4Mod. Amino AcidD-VALINE
4ETA2Mod. Amino AcidETHANOLAMINE
5FVA2Mod. Amino AcidN-FORMYL-L-VALINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:9 , DLE A:10 , TRP A:11 , TRP B:9 , DLE B:10 , TRP B:11 , TRP C:9 , TRP C:13 , DLE D:10 , TRP D:15 , TRP E:9 , TRP E:13 , DLE F:10 , TRP F:15BINDING SITE FOR RESIDUE 15P A1001
2AC2SOFTWARETRP A:15 , ETA A:16 , DLE B:4 , DLE C:4 , TRP D:15 , ETA D:16 , TRP E:15BINDING SITE FOR RESIDUE 15P A1002
3AC3SOFTWAREFVA B:1 , TRP D:15 , ETA D:16BINDING SITE FOR RESIDUE 15P A1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y5M)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y5M)

(-) 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 .eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2y5m 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 ---------------- 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
                  2y5m 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 ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2y5m 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 ---------------- 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
                  2y5m D  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain E from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  2y5m E  1 xGAxAxVxWxWxWxWx 16
                            |  | | |10 | | |
                            |  | | | | | | |
                            1-FVA| | | | | |
                               4-DLE | | | |
                                 6-DVA | | |
                                   8-DVA | |
                                    10-DLE |
                                      12-DLE
                                        14-DLE
                                          16-ETA


Chain F from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- 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
                  2y5m F  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  (0, 0)

(no "SCOP Domain" information available for 2Y5M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y5M)

(-) Gene Ontology  (0, 0)

Asymmetric 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 GRAMICIDIN D FROM BACILLUS BREVIS (N- PROPANOL SOLVATE)
1alx GRAMICIDIN D FROM BACILLUS BREVIS (METHANOL SOLVATE)
1alz GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
1av2 GRAMICIDIN A/CSCL COMPLEX, ACTIVE AS A DIMER
1bdw GRAMICIDIN D FROM BACILLUS BREVIS (ACTIVE FORM)
1c4d GRAMICIDIN CSCL COMPLEX
1gmk GRAMICIDIN/KSCN COMPLEX
1grm GRAMICIDIN A (NMR, 5 STRUCTURES)
1jno GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES (NMR)
1jo3 GRAMICIDIN B IN SODIUM DODECYL SULFATE MICELLES (NMR)
1jo4 GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES (NMR)
1kqe SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A INBENZENE/ACETONE 10:1
1mag GRAMICIDIN A IN HYDRATED DMPC BILAYERS, SOLID STATE NMR
1mic GRAMICIDIN A: LEFT-HANDED PARALLEL DOUBLE HELICAL FORM IN METHANOL IN THE PRESENCE OF CACL2, NMR, 20 STRUCTURES
1ng8 G15-GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES (NMR)
1nrm GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES (NMR)
1nru GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES IN THEPRESENCE OF EXCESS NA+ (NMR)
1nt5 F1-GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES (NMR)
1nt6 F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES (NMR)
1tkq SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN IN AMEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE IN THE PRESENCE OFCSCL
1w5u GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
2izq GRAMICIDIN D COMPLEX WITH KI
2xdc STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A LIPID CUBIC PHASE.
2y6n STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A 8.8 MONOACYLGLYCEROL LIPID CUBIC PHASE.