3RAV - JenaLib

Title :   HORSE SPLEEN APO-FERRITIN WITH BOUND PENTOBARBITAL

Authors :   S. H. Oakley, L. S. Vedula, J. Xi, R. Liu, R. G. Eckenhoff, P. J. Loll

Date :   28 Mar 11 (Deposition) - 11 May 11 (Release) - 11 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: A  (4x)
Biol. Unit 4: A  (24x)

Keywords :   4-Helix Bundle, Iron, Iron Storage, Metal-Binding, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. H. Oakley, L. S. Vedula, J. Xi, R. Liu, R. G. Eckenhoff, P. J. Loll
High Resolution View Of Barbiturate Recognition By A Protei Binding Site
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CD	6	Ligand/Ion	CADMIUM ION
2	RAV	1	Ligand/Ion	5-ETHYL-5-[(2S)-PENTAN-2-YL]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	RAV	1	Ligand/Ion	5-ETHYL-5-[(2S)-PENTAN-2-YL]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	RAV	2	Ligand/Ion	5-ETHYL-5-[(2S)-PENTAN-2-YL]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	RAV	4	Ligand/Ion	5-ETHYL-5-[(2S)-PENTAN-2-YL]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 72)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	RAV	24	Ligand/Ion	5-ETHYL-5-[(2S)-PENTAN-2-YL]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE
3	SO4	48	Ligand/Ion	SULFATE ION

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:80 , GLN A:82	BINDING SITE FOR RESIDUE CD A 175
2	AC2	SOFTWARE	GLU A:56 , GLU A:57 , GLU A:60 , HOH A:276 , HOH A:285	BINDING SITE FOR RESIDUE CD A 176
3	AC3	SOFTWARE	GLU A:53 , GLU A:56 , HOH A:283	BINDING SITE FOR RESIDUE CD A 177
4	AC4	SOFTWARE	ASP A:127	BINDING SITE FOR RESIDUE CD A 178
5	AC5	SOFTWARE	GLU A:130 , HOH A:277	BINDING SITE FOR RESIDUE CD A 179
6	AC6	SOFTWARE	GLN A:6 , ASN A:7 , HOH A:239 , HOH A:244 , HOH A:297 , HOH A:318	BINDING SITE FOR RESIDUE SO4 A 180
7	AC7	SOFTWARE	LYS A:143 , ASP A:146 , HIS A:147 , HOH A:265 , HOH A:266 , HOH A:278 , HOH A:324 , HOH A:362	BINDING SITE FOR RESIDUE SO4 A 181
8	AC8	SOFTWARE	GLU A:11	BINDING SITE FOR RESIDUE CD A 182
9	AC9	SOFTWARE	LEU A:24 , SER A:27 , TYR A:28 , ALA A:55 , ARG A:59 , LEU A:81	BINDING SITE FOR RESIDUE RAV A 183

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	A:6-155
2	FERRITIN_1	PS00540	Ferritin iron-binding regions signature 1.	FRIL_HORSE	58-76	1	A:57-75
3	FERRITIN_2	PS00204	Ferritin iron-binding regions signature 2.	FRIL_HORSE	123-143	1	A:122-142

Biological Unit 1 (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	A:6-155
2	FERRITIN_1	PS00540	Ferritin iron-binding regions signature 1.	FRIL_HORSE	58-76	1	A:57-75
3	FERRITIN_2	PS00204	Ferritin iron-binding regions signature 2.	FRIL_HORSE	123-143	1	A:122-142

Biological Unit 2 (3, 6)

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

Biological Unit 3 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FERRITIN_LIKE	PS50905	Ferritin-like diiron domain profile.	FRIL_HORSE	7-156	4	A:6-155
2	FERRITIN_1	PS00540	Ferritin iron-binding regions signature 1.	FRIL_HORSE	58-76	4	A:57-75
3	FERRITIN_2	PS00204	Ferritin iron-binding regions signature 2.	FRIL_HORSE	123-143	4	A:122-142

Biological Unit 4 (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	A:6-155
2	FERRITIN_1	PS00540	Ferritin iron-binding regions signature 1.	FRIL_HORSE	58-76	24	A:57-75
3	FERRITIN_2	PS00204	Ferritin iron-binding regions signature 2.	FRIL_HORSE	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

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Chain A from PDB  Type:PROTEIN  Length:168
 aligned with FRIL_HORSE | P02791 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
           FRIL_HORSE     3 SQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTL 172
               SCOP domains d3rava_ A: (Apo)ferritin                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Ferritin-3ravA01 A:13-154                                                                                                                     ----------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--hhhhhhhhhhhhh. 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
                 3rav A   2 SQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLV--QAGLGEYLFERLTL 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   |  |161       171
                                                                                                                                                                                   155  |             
                                                                                                                                                                                      158

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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A (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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