2ZG9 - JenaLib

Title :   CRYSTAL STRUCTURE OF PD(ALLYL)/APO-H114AFR

Authors :   S. Abe, J. Niemeyer, M. Abe, T. Ueno, T. Hikage, G. Erker, Y. Watanabe

Date :   18 Jan 08 (Deposition) - 26 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Iron Storage Protein, Light Chain Apoferritin, Artificial Metalloprotein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Abe, J. Niemeyer, M. Abe, Y. Takezawa, T. Ueno, T. Hikage, G. Erker, Y. Watanabe
Control Of The Coordination Structure Of Organometallic Palladium Complexes In An Apo-Ferritin Cage.
J. Am. Chem. Soc. V. 130 10512 2008
PubMed-ID: 18636721 | Reference-DOI: 10.1021/JA802463A
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP X:80 , GLN X:82 , HOH X:286	BINDING SITE FOR RESIDUE CD X 175
02	AC2	SOFTWARE	GLN X:86 , ASP X:87 , GLU X:88 , HOH X:255 , HOH X:391	BINDING SITE FOR RESIDUE SO4 X 176
03	AC3	SOFTWARE	LYS X:143 , ASP X:146 , HIS X:147 , HOH X:209 , HOH X:266 , HOH X:268 , HOH X:311 , HOH X:335	BINDING SITE FOR RESIDUE SO4 X 177
04	AC4	SOFTWARE	GLN X:6 , ASN X:7 , HOH X:227 , HOH X:259 , HOH X:264 , HOH X:284	BINDING SITE FOR RESIDUE SO4 X 178
05	AC5	SOFTWARE	GLU X:45 , HIS X:49 , ARG X:168 , HIS X:173 , HOH X:311 , HOH X:359	BINDING SITE FOR RESIDUE SO4 X 179
06	AC6	SOFTWARE	CYS X:126 , GLU X:130	BINDING SITE FOR RESIDUE PLL X 180
07	AC7	SOFTWARE	ASP X:38 , GLU X:45 , CYS X:48 , LYS X:67	BINDING SITE FOR RESIDUE PLL X 181
08	AC8	SOFTWARE	CYS X:48 , HIS X:49 , ARG X:52	BINDING SITE FOR RESIDUE PLL X 182
09	AC9	SOFTWARE	TYR X:36 , GLY X:90 , THR X:91 , ARG X:153 , GLU X:163 , HOH X:276 , HOH X:330	BINDING SITE FOR RESIDUE EDO X 183
10	BC1	SOFTWARE	ALA X:14 , ASN X:17 , ARG X:18 , HOH X:238 , HOH X:252 , HOH X:332	BINDING SITE FOR RESIDUE EDO X 184
11	BC2	SOFTWARE	THR X:10 , GLU X:11 , ALA X:14 , HOH X:210 , HOH X:293 , HOH X:322	BINDING SITE FOR RESIDUE EDO X 185
12	BC3	SOFTWARE	ARG X:25 , GLN X:82 , LYS X:83 , SER X:85 , HOH X:298 , HOH X:390	BINDING SITE FOR RESIDUE EDO X 186
13	BC4	SOFTWARE	HIS X:49 , HOH X:359	BINDING SITE FOR RESIDUE EDO X 187
14	BC5	SOFTWARE	SER X:27 , GLU X:56 , ARG X:59 , HOH X:305	BINDING SITE FOR RESIDUE EDO X 188

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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.	FRIL_HORSE	7-156	1	X:6-155
2	FERRITIN_1	PS00540	Ferritin iron-binding regions signature 1.	FRIL_HORSE	58-76	1	X:57-75
3	FERRITIN_2	PS00204	Ferritin iron-binding regions signature 2.	FRIL_HORSE	123-143	1	X: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.	FRIL_HORSE	7-156	24	X:6-155
2	FERRITIN_1	PS00540	Ferritin iron-binding regions signature 1.	FRIL_HORSE	58-76	24	X:57-75
3	FERRITIN_2	PS00204	Ferritin iron-binding regions signature 2.	FRIL_HORSE	123-143	24	X: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
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Chain X from PDB  Type:PROTEIN  Length:173
 aligned with FRIL_HORSE | P02791 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:173
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171   
           FRIL_HORSE     2 SSQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTLKH 174
               SCOP domains d2zg9x_ X: (Apo)ferritin                                                                                                                                                      SCOP domains
               CATH domains 2zg9X00 X:1-173  [code=1.20.1260.10, no name defined]                                                                                                                         CATH domains
               Pfam domains ------------Ferritin-2zg9X01 X:13-154                                                                                                                     ------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----FERRITIN_LIKE  PDB: X:6-155 UniProt: 7-156                                                                                                            ------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------FERRITIN_1         ----------------------------------------------FERRITIN_2           ------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zg9 X   1 SSQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTPDAMKAAIVLEKSLNQALLDLAALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTLKH 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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	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 (1, 1)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain X (FRIL_HORSE | P02791)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.
cellular component
	GO:0008043	intracellular ferritin complex	A ferritin complex located in the cell. Intracellular ferritin complexes contain 24 subunits, in a mixture of L (light) chains and H (heavy) chains.

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