4W6U - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FULL-LENGTH SPLIT GFP MUTANT E115H/T118H WITH NICKEL MEDIATED CRYSTAL CONTACTS, P 21 21 21 SPACE GROUP

Authors :   D. J. Leibly, G. S. Waldo, T. O. Yeates

Date :   20 Aug 14 (Deposition) - 18 Feb 15 (Release) - 27 Jan 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Leibly, M. A. Arbing, I. Pashkov, N. Devore, G. S. Waldo, T. C. Terwilliger, T. O. Yeates
A Suite Of Engineered Gfp Molecules For Oligomeric Scaffolding.
Structure V. 23 1754 2015
PubMed-ID: 26278175 | Reference-DOI: 10.1016/J.STR.2015.07.008

Molecule 1 - FLUORESCENT PROTEIN E115H/T118H
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	CRO	4	Mod. Amino Acid	{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	NI	2	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CIT	-1	Ligand/Ion	CITRIC ACID
2	CRO	1	Mod. Amino Acid	{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	-1	Ligand/Ion	CITRIC ACID
2	CRO	1	Mod. Amino Acid	{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	CRO	1	Mod. Amino Acid	{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	-1	Ligand/Ion	CITRIC ACID
2	CRO	1	Mod. Amino Acid	{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:25 , HOH A:403 , HOH A:405	binding site for residue NI A 301
2	AC2	SOFTWARE	TYR A:182	binding site for residue EDO A 302
3	AC3	SOFTWARE	TYR A:151 , THR A:153 , ASN A:164 , ASP B:102	binding site for residue EDO A 303
4	AC4	SOFTWARE	HIS A:118 , HOH A:404 , HOH A:408 , HIS B:115 , HOH B:415	binding site for residue NI B 301
5	AC5	SOFTWARE	GLU C:32 , GLY C:33 , HIS C:118	binding site for residue CIT C 301

(no "SS Bond" information available for 4W6U)

Asymmetric Unit

No.	Residues
1	Met A:88	-	Pro A:89
2	Met B:88	-	Pro B:89
3	Met C:88	-	Pro C:89
4	Met D:88	-	Pro D:89

(no "SAP(SNP)/Variant" information available for 4W6U)

(no "PROSITE Motif" information available for 4W6U)

(no "Exon" information available for 4W6U)

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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6u A   3 KGEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFHGDHLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGI 229
                                    12        22        32        42        52        62 |||    74        84        94       104       114       124       134       144       154       164       174       184     ||196       206       216       226   
                                                                                        64||                                                                                                                       190|                                    
                                                                                         66-CRO                                                                                                                     193                                    
                                                                                          68

Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4w6u B   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFHGDHLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAA 227
                                    13        23        33        43        53        63|||     75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225  
                                                                                       64||                                                                                                                                                               
                                                                                        66-CRO                                                                                                                                                            
                                                                                         68

Chain C from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4w6u C   3 KGEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFHGDHLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGPVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAG 228
                                    12        22        32        42        52        62 |||    74        84        94       104       114       124       134       144       154       164       174       184    || 196       206       216       226  
                                                                                        64||                                                                                                                      189|                                    
                                                                                         66-CRO                                                                                                                    192                                    
                                                                                          68

Chain D from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6u D   3 KGEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFHGDHLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAG 228
                                    12        22        32        42        52        62 |||    74        84        94       104       114       124       134       144       154       164       174       184      |195       205       215       225   
                                                                                        64||                                                                                                                        191|                                   
                                                                                         66-CRO                                                                                                                      193                                   
                                                                                          68

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 '\|'

(no "SCOP Domain" information available for 4W6U)

(no "CATH Domain" information available for 4W6U)

(no "Pfam Domain" information available for 4W6U)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 4W6U)

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
		CIT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CRO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NI	[ 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 ]

	Cis Peptide Bonds
		Met A:88 - Pro A:89	[ RasMol ]
		Met B:88 - Pro B:89	[ RasMol ]
		Met C:88 - Pro C:89	[ RasMol ]
		Met D:88 - Pro D:89	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

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 \| Biol. Unit 3 PNG format \| Biol. Unit 4 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)

Access by PDB/NDB ID
	4w6u
		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

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

(no "Entries Sharing at Least One Protein Chain" available for 4W6U)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File