1C4D - JenaLib

Title :   GRAMICIDIN CSCL COMPLEX

Authors :   B. A. Wallace

Date :   04 Jun 99 (Deposition) - 03 Jan 00 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Antibiotic, Gramicidin, Antifungal, Antibacterial, Double Helix, Membrane Ion Channel, Linear Gramicidin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Wallace, K. Ravikumar
The Gramicidin Pore: Crystal Structure Of A Cesium Complex.
Science V. 241 182 1988
PubMed-ID: 2455344 | Reference-DOI: 10.1126/SCIENCE.2455344
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 59)

Asymmetric Unit (7, 59)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	CS	8	Ligand/Ion	CESIUM ION
3	DLE	16	Mod. Amino Acid	D-LEUCINE
4	DVA	8	Mod. Amino Acid	D-VALINE
5	ETA	4	Mod. Amino Acid	ETHANOLAMINE
6	FVA	4	Mod. Amino Acid	N-FORMYL-L-VALINE
7	MOH	13	Ligand/Ion	METHANOL

Biological Unit 1 (5, 23)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CS	-1	Ligand/Ion	CESIUM ION
3	DLE	8	Mod. Amino Acid	D-LEUCINE
4	DVA	4	Mod. Amino Acid	D-VALINE
5	ETA	2	Mod. Amino Acid	ETHANOLAMINE
6	FVA	2	Mod. Amino Acid	N-FORMYL-L-VALINE
7	MOH	7	Ligand/Ion	METHANOL

Biological Unit 2 (5, 22)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CS	-1	Ligand/Ion	CESIUM ION
3	DLE	8	Mod. Amino Acid	D-LEUCINE
4	DVA	4	Mod. Amino Acid	D-VALINE
5	ETA	2	Mod. Amino Acid	ETHANOLAMINE
6	FVA	2	Mod. Amino Acid	N-FORMYL-L-VALINE
7	MOH	6	Ligand/Ion	METHANOL

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:5 , DVA A:6 , VAL A:7 , TRP B:9 , DLE B:10 , TRP B:11	BINDING SITE FOR RESIDUE CS A 116
02	AC2	SOFTWARE	DLE A:14 , DLE C:14	BINDING SITE FOR RESIDUE CS A 117
03	AC3	SOFTWARE	VAL A:7 , TRP D:13	BINDING SITE FOR RESIDUE CS A 118
04	AC4	SOFTWARE	TRP A:9 , DLE A:10 , ALA B:5 , DVA B:6 , VAL B:7 , DVA B:8	BINDING SITE FOR RESIDUE CL A 119
05	AC5	SOFTWARE	ALA A:3 , DLE A:4 , TRP B:13 , DLE B:14	BINDING SITE FOR RESIDUE CL A 120
06	AC6	SOFTWARE	DLE A:14 , HOH A:2001 , ALA B:3 , DLE B:4 , ALA B:5 , HOH B:2003	BINDING SITE FOR RESIDUE CS B 116
07	AC7	SOFTWARE	HOH A:2003 , GLY B:2 , ALA B:3 , HOH B:2003	BINDING SITE FOR RESIDUE CL B 117
08	AC8	SOFTWARE	TRP C:11 , DLE C:12 , TRP C:13 , DLE C:14 , ALA D:5 , DVA D:6 , CL D:119	BINDING SITE FOR RESIDUE CS C 116
09	AC9	SOFTWARE	VAL C:7 , DVA C:8 , TRP C:9 , DLE C:10 , VAL D:7 , DVA D:8	BINDING SITE FOR RESIDUE CL C 117
10	BC1	SOFTWARE	GLY C:2 , ALA C:3 , DLE C:4 , TRP D:15 , ETA D:16	BINDING SITE FOR RESIDUE CL C 118
11	BC2	SOFTWARE	ALA C:3 , ALA C:5 , TRP D:11 , DLE D:12 , TRP D:13 , DLE D:14	BINDING SITE FOR RESIDUE CS D 116
12	BC3	SOFTWARE	GLY B:2 , ALA B:3	BINDING SITE FOR RESIDUE CS D 117
13	BC4	SOFTWARE	DLE C:4 , DLE C:10 , DLE D:10	BINDING SITE FOR RESIDUE CS D 118
14	BC5	SOFTWARE	CS C:116 , HOH C:2003 , GLY D:2 , ALA D:3	BINDING SITE FOR RESIDUE CL D 119
15	BC6	SOFTWARE	CS A:116 , CS A:117 , CS A:118 , CL A:119 , CL A:120 , HOH A:2001 , HOH A:2003 , 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 , CS B:116 , CL B:117 , HOH B:2001 , HOH B:2002 , HOH B:2005 , HOH B:2006 , DLE C:4 , TRP C:9 , TRP C:11 , TRP C:13 , TRP C:15 , HOH C:2001 , TRP D:9 , DLE D:14	BINDING SITE FOR CHAIN A OF GRAMICIDIN A
16	BC7	SOFTWARE	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 , CS A:116 , CS A:117 , CL A:119 , CL A:120 , HOH A:2001 , HOH A:2003 , CS B:116 , CL B:117 , HOH B:2001 , HOH B:2002 , HOH B:2003 , HOH B:2005 , HOH B:2006 , DVA C:6 , TRP C:9 , DLE C:10 , TRP C:11 , DVA D:8 , TRP D:11 , CS D:117	BINDING SITE FOR CHAIN B OF GRAMICIDIN A
17	BC8	SOFTWARE	DLE A:4 , ALA A:5 , TRP A:11 , TRP A:13 , TRP A:15 , CS A:117 , TRP B:9 , TRP B:11 , DLE B:14 , HOH B:2006 , CS C:116 , CL C:117 , CL C:118 , HOH C:2001 , HOH C:2003 , 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 , CS D:116 , CS D:118 , HOH D:2001 , HOH D:2002	BINDING SITE FOR CHAIN C OF GRAMICIDIN A
18	BC9	SOFTWARE	TRP A:9 , TRP A:11 , CS A:118 , DVA B:8 , TRP B:11 , 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 , CS C:116 , CL C:117 , CL C:118 , HOH C:2001 , HOH C:2003 , CS D:116 , CS D:118 , CL D:119 , HOH D:2001 , HOH D:2002	BINDING SITE FOR CHAIN D OF GRAMICIDIN A

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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 d1c4da_ A:       SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ...eeeeeee.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  1c4d 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 d1c4db_ B:       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
                  1c4d 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 d1c4dc_ C:       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
                  1c4d 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 d1c4dd_ D:       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
                  1c4d 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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DLE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DVA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ETA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FVA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MOH	[ 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 ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1c4d)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1c4d
		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

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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
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

Description