3KA6 - JenaLib

Title :   FROG M-FERRITIN, EED MUTANT, WITH COBALT

Authors :   T. Tosha, H. L. Ng, E. Theil, T. Alber, O. Bhattasali

Date :   18 Oct 09 (Deposition) - 06 Oct 10 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (24x)

Keywords :   Iron Storage, Diiron, Iron, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Tosha, H. L. Ng, O. Bhattasali, T. Alber, E. C. Theil
Moving Metal Ions Through Ferritin-Protein Nanocages From Three-Fold Pores To Catalytic Sites.
J. Am. Chem. Soc. V. 132 14562 2010
PubMed-ID: 20866049 | Reference-DOI: 10.1021/JA105583D

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (19, 19)

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:169 , CL A:189 , HOH A:430	BINDING SITE FOR RESIDUE CO A 176
02	AC2	SOFTWARE	GLU A:23 , GLU A:58 , HIS A:61 , CO A:178 , HOH A:386 , HOH A:387	BINDING SITE FOR RESIDUE CO A 177
03	AC3	SOFTWARE	HIS A:54 , GLU A:58 , GLU A:103 , CO A:177 , CO A:184 , HOH A:347 , HOH A:387 , HOH A:491	BINDING SITE FOR RESIDUE CO A 178
04	AC4	SOFTWARE	HIS A:56 , GLU A:60 , GLU A:63 , HOH A:469 , HOH A:489	BINDING SITE FOR RESIDUE CO A 179
05	AC5	SOFTWARE	HOH A:352 , HOH A:411	BINDING SITE FOR RESIDUE CO A 180
06	AC6	SOFTWARE	ASP A:41 , HOH A:238 , HOH A:252 , HOH A:264 , HOH A:332 , HOH A:433	BINDING SITE FOR RESIDUE CO A 181
07	AC7	SOFTWARE	HIS A:45 , GLU A:49 , HOH A:259 , HOH A:336 , HOH A:337	BINDING SITE FOR RESIDUE CO A 182
08	AC8	SOFTWARE	GLU A:57 , GLU A:136 , ASP A:140 , CO A:184 , HOH A:294 , HOH A:338 , HOH A:345 , HOH A:349 , HOH A:507	BINDING SITE FOR RESIDUE CO A 183
09	AC9	SOFTWARE	HIS A:54 , ASP A:140 , CO A:178 , CO A:183 , HOH A:344 , HOH A:345 , HOH A:347 , HOH A:349 , HOH A:491	BINDING SITE FOR RESIDUE CO A 184
10	BC1	SOFTWARE	ASP A:127 , HOH A:250 , HOH A:342	BINDING SITE FOR RESIDUE CO A 185
11	BC2	SOFTWARE	HOH A:361 , HOH A:379 , HOH A:392 , HOH A:406	BINDING SITE FOR RESIDUE MG A 186
12	BC3	SOFTWARE	SER A:10 , HOH A:235 , HOH A:376 , HOH A:440 , HOH A:444 , HOH A:493	BINDING SITE FOR RESIDUE MG A 187
13	BC4	SOFTWARE	HOH A:213 , HOH A:304 , HOH A:315 , HOH A:333 , HOH A:396 , HOH A:490	BINDING SITE FOR RESIDUE MG A 188
14	BC5	SOFTWARE	LEU A:165 , HIS A:169 , CO A:176	BINDING SITE FOR RESIDUE CL A 189
15	BC6	SOFTWARE	SER A:131 , GLU A:132 , TYR A:133 , GLU A:135 , GLU A:136 , HOH A:511	BINDING SITE FOR RESIDUE CL A 190
16	BC7	SOFTWARE	HOH A:253 , HOH A:299 , HOH A:323 , HOH A:334 , HOH A:473 , HOH A:515	BINDING SITE FOR RESIDUE MG A 191
17	BC8	SOFTWARE	HOH A:340 , HOH A:341 , HOH A:414 , HOH A:461	BINDING SITE FOR RESIDUE MG A 192
18	BC9	SOFTWARE	ARG A:5 , ASN A:7 , TYR A:8 , HOH A:302	BINDING SITE FOR RESIDUE CL A 193
19	CC1	SOFTWARE	SER A:10 , HOH A:293	BINDING SITE FOR RESIDUE CL A 194

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	FRI2_LITCT	7-156	1	A:6-155
2	FERRITIN_1	PS00540	Ferritin iron-binding regions signature 1.	FRI2_LITCT	58-76	1	A:57-75
3	FERRITIN_2	PS00204	Ferritin iron-binding regions signature 2.	FRI2_LITCT	123-143	1	A:122-142

Biological Unit 1 (3, 72)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	FRI2_LITCT	7-156	24	A:6-155
2	FERRITIN_1	PS00540	Ferritin iron-binding regions signature 1.	FRI2_LITCT	58-76	24	A:57-75
3	FERRITIN_2	PS00204	Ferritin iron-binding regions signature 2.	FRI2_LITCT	123-143	24	A:122-142

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:172
 aligned with FRI2_LITCT | P07798 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171  
           FRI2_LITCT     2 VSQVRQNYHSDCEAAVNRMLNLELYASYTYSSMYAFFDRDDVALHNVAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIKKPERDEWGNTLEAMQAALQLEKTVNQALLDLHKLATDKVDPHLCDFLESEYLEEQVKDIKRIGDFITNLKRLGLPENGMGEYLFDKHSVK 173
               SCOP domains d3ka6a_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----FERRITIN_LIKE  PDB: A:6-155 UniProt: 7-156                                                                                                            ----------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------FERRITIN_1         ----------------------------------------------FERRITIN_2           ------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ka6 A   1 VSQVRQNYHSDCEAAVNRMLNLELYASYTYSSMYAFFDRDDVALHNVAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIKKPERDEWGNTLEAMQAALQLEKTVNQALLDLHKLATDKVDPHLCDFLESEYLEEEVKDIKRIGDFITNLKRLGLPENGMGEYLFDKHSVK 172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (FRI2_LITCT | P07798)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0004322	ferroxidase activity	Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0006826	iron ion transport	The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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 ]
		CO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ 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 ]
		CC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:156 - Pro A:157	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3ka6
		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
	FRI2_LITCT \| P07798
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.16.3.1
		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
	FRI2_LITCT \| P07798
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description