2YGJ - JenaLib

Title :   METHANOBACTIN MB4

Authors :   A. Ghazouani, A. Basle, S. J. Firbank, J. Gray, C. Dennison

Date :   18 Apr 11 (Deposition) - 25 Apr 12 (Release) - 03 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.80

Chains :   Asym./Biol. Unit : A

Keywords :   Metal Transport, Methanotrophs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. El Ghazouani, A. Basle, J. Gray, D. W. Graham, S. J. Firbank, C. Dennison
Variations In Methanobactin Structure Influences Copper Utilization By Methane-Oxidizing Bacteria.
Proc. Natl. Acad. Sci. Usa V. 109 8400 2012
PubMed-ID: 22582172 | Reference-DOI: 10.1073/PNAS.1112921109

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	CU	1	Ligand/Ion	COPPER (II) ION
2	HM8	1	Mod. Amino Acid	2-[(1S,2R)-1-AMINO-2-(SULFOOXY)PROPYL]-5-HYDROXY-1,3-OXAZOLE-4-CARBOTHIOIC O-ACID
3	HM9	1	Mod. Amino Acid	6-(3-CARBAMIMIDAMIDOPROPYL)-3,5-DIHYDROXYPYRAZINE-2-CARBOTHIOIC S-ACID
4	NA	2	Ligand/Ion	SODIUM ION

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HM9 A:1 , HM8 A:4	BINDING SITE FOR RESIDUE CU A1007
2	AC2	SOFTWARE	HM8 A:4 , MET A:6 , NA A:1009 , HOH A:2002 , HOH A:2004 , HOH A:2010 , HOH A:2011	BINDING SITE FOR RESIDUE NA A1008
3	AC3	SOFTWARE	HM8 A:4 , MET A:6 , NA A:1008 , HOH A:2009 , HOH A:2010 , HOH A:2012 , HOH A:2013	BINDING SITE FOR RESIDUE NA A1009

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/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:6
                                    
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                   2ygj A 1 xASxAM 6
                            |  |  
                            |  |  
                            1-HM9 
                               4-HM8

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Asymmetric/Biological 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
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HM8	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HM9	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ygj)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	2ygj
		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

Description