Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5UP9

Crystal Structure of Zn-bound Human Heavy-Chain ferritin variant 122H-delta C-star with para-xylenedihydroxamate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004322	molecular_function	ferroxidase activity
A	0005506	molecular_function	iron ion binding
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005764	cellular_component	lysosome
A	0005776	cellular_component	autophagosome
A	0005829	cellular_component	cytosol
A	0006826	biological_process	iron ion transport
A	0006879	biological_process	intracellular iron ion homeostasis
A	0006955	biological_process	immune response
A	0008198	molecular_function	ferrous iron binding
A	0008199	molecular_function	ferric iron binding
A	0008285	biological_process	negative regulation of cell population proliferation
A	0016491	molecular_function	oxidoreductase activity
A	0031410	cellular_component	cytoplasmic vesicle
A	0042802	molecular_function	identical protein binding
A	0044754	cellular_component	autolysosome
A	0046872	molecular_function	metal ion binding
A	0048147	biological_process	negative regulation of fibroblast proliferation
A	0070062	cellular_component	extracellular exosome
A	0070288	cellular_component	ferritin complex
A	0110076	biological_process	negative regulation of ferroptosis
A	0140315	molecular_function	iron ion sequestering activity
A	1904724	cellular_component	tertiary granule lumen
A	1904813	cellular_component	ficolin-1-rich granule lumen
B	0004322	molecular_function	ferroxidase activity
B	0005506	molecular_function	iron ion binding
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005764	cellular_component	lysosome
B	0005776	cellular_component	autophagosome
B	0005829	cellular_component	cytosol
B	0006826	biological_process	iron ion transport
B	0006879	biological_process	intracellular iron ion homeostasis
B	0006955	biological_process	immune response
B	0008198	molecular_function	ferrous iron binding
B	0008199	molecular_function	ferric iron binding
B	0008285	biological_process	negative regulation of cell population proliferation
B	0016491	molecular_function	oxidoreductase activity
B	0031410	cellular_component	cytoplasmic vesicle
B	0042802	molecular_function	identical protein binding
B	0044754	cellular_component	autolysosome
B	0046872	molecular_function	metal ion binding
B	0048147	biological_process	negative regulation of fibroblast proliferation
B	0070062	cellular_component	extracellular exosome
B	0070288	cellular_component	ferritin complex
B	0110076	biological_process	negative regulation of ferroptosis
B	0140315	molecular_function	iron ion sequestering activity
B	1904724	cellular_component	tertiary granule lumen
B	1904813	cellular_component	ficolin-1-rich granule lumen
C	0004322	molecular_function	ferroxidase activity
C	0005506	molecular_function	iron ion binding
C	0005515	molecular_function	protein binding
C	0005576	cellular_component	extracellular region
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005764	cellular_component	lysosome
C	0005776	cellular_component	autophagosome
C	0005829	cellular_component	cytosol
C	0006826	biological_process	iron ion transport
C	0006879	biological_process	intracellular iron ion homeostasis
C	0006955	biological_process	immune response
C	0008198	molecular_function	ferrous iron binding
C	0008199	molecular_function	ferric iron binding
C	0008285	biological_process	negative regulation of cell population proliferation
C	0016491	molecular_function	oxidoreductase activity
C	0031410	cellular_component	cytoplasmic vesicle
C	0042802	molecular_function	identical protein binding
C	0044754	cellular_component	autolysosome
C	0046872	molecular_function	metal ion binding
C	0048147	biological_process	negative regulation of fibroblast proliferation
C	0070062	cellular_component	extracellular exosome
C	0070288	cellular_component	ferritin complex
C	0110076	biological_process	negative regulation of ferroptosis
C	0140315	molecular_function	iron ion sequestering activity
C	1904724	cellular_component	tertiary granule lumen
C	1904813	cellular_component	ficolin-1-rich granule lumen
D	0004322	molecular_function	ferroxidase activity
D	0005506	molecular_function	iron ion binding
D	0005515	molecular_function	protein binding
D	0005576	cellular_component	extracellular region
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005764	cellular_component	lysosome
D	0005776	cellular_component	autophagosome
D	0005829	cellular_component	cytosol
D	0006826	biological_process	iron ion transport
D	0006879	biological_process	intracellular iron ion homeostasis
D	0006955	biological_process	immune response
D	0008198	molecular_function	ferrous iron binding
D	0008199	molecular_function	ferric iron binding
D	0008285	biological_process	negative regulation of cell population proliferation
D	0016491	molecular_function	oxidoreductase activity
D	0031410	cellular_component	cytoplasmic vesicle
D	0042802	molecular_function	identical protein binding
D	0044754	cellular_component	autolysosome
D	0046872	molecular_function	metal ion binding
D	0048147	biological_process	negative regulation of fibroblast proliferation
D	0070062	cellular_component	extracellular exosome
D	0070288	cellular_component	ferritin complex
D	0110076	biological_process	negative regulation of ferroptosis
D	0140315	molecular_function	iron ion sequestering activity
D	1904724	cellular_component	tertiary granule lumen
D	1904813	cellular_component	ficolin-1-rich granule lumen
E	0004322	molecular_function	ferroxidase activity
E	0005506	molecular_function	iron ion binding
E	0005515	molecular_function	protein binding
E	0005576	cellular_component	extracellular region
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005764	cellular_component	lysosome
E	0005776	cellular_component	autophagosome
E	0005829	cellular_component	cytosol
E	0006826	biological_process	iron ion transport
E	0006879	biological_process	intracellular iron ion homeostasis
E	0006955	biological_process	immune response
E	0008198	molecular_function	ferrous iron binding
E	0008199	molecular_function	ferric iron binding
E	0008285	biological_process	negative regulation of cell population proliferation
E	0016491	molecular_function	oxidoreductase activity
E	0031410	cellular_component	cytoplasmic vesicle
E	0042802	molecular_function	identical protein binding
E	0044754	cellular_component	autolysosome
E	0046872	molecular_function	metal ion binding
E	0048147	biological_process	negative regulation of fibroblast proliferation
E	0070062	cellular_component	extracellular exosome
E	0070288	cellular_component	ferritin complex
E	0110076	biological_process	negative regulation of ferroptosis
E	0140315	molecular_function	iron ion sequestering activity
E	1904724	cellular_component	tertiary granule lumen
E	1904813	cellular_component	ficolin-1-rich granule lumen
F	0004322	molecular_function	ferroxidase activity
F	0005506	molecular_function	iron ion binding
F	0005515	molecular_function	protein binding
F	0005576	cellular_component	extracellular region
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005764	cellular_component	lysosome
F	0005776	cellular_component	autophagosome
F	0005829	cellular_component	cytosol
F	0006826	biological_process	iron ion transport
F	0006879	biological_process	intracellular iron ion homeostasis
F	0006955	biological_process	immune response
F	0008198	molecular_function	ferrous iron binding
F	0008199	molecular_function	ferric iron binding
F	0008285	biological_process	negative regulation of cell population proliferation
F	0016491	molecular_function	oxidoreductase activity
F	0031410	cellular_component	cytoplasmic vesicle
F	0042802	molecular_function	identical protein binding
F	0044754	cellular_component	autolysosome
F	0046872	molecular_function	metal ion binding
F	0048147	biological_process	negative regulation of fibroblast proliferation
F	0070062	cellular_component	extracellular exosome
F	0070288	cellular_component	ferritin complex
F	0110076	biological_process	negative regulation of ferroptosis
F	0140315	molecular_function	iron ion sequestering activity
F	1904724	cellular_component	tertiary granule lumen
F	1904813	cellular_component	ficolin-1-rich granule lumen

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue ZN A 201

Chain	Residue
A	GLU27
A	GLU62
A	HIS65
A	ZN202
A	HOH322
A	HOH327

site_id	AC2
Number of Residues	5
Details	binding site for residue ZN A 202

Chain	Residue
A	HOH327
A	HOH397
A	GLU62
A	GLU107
A	ZN201

site_id	AC3
Number of Residues	5
Details	binding site for residue ZN A 203

Chain	Residue
A	HIS173
A	HOH390
D	HIS173
E	HIS173
F	HIS173

site_id	AC4
Number of Residues	6
Details	binding site for residue ZN A 204

Chain	Residue
A	ASP131
A	GLU134
B	ASP131
B	GLU134
F	ASP131
F	GLU134

site_id	AC5
Number of Residues	5
Details	binding site for residue PGE A 205

Chain	Residue
A	ASN25
A	TYR29
A	ILE85
A	GLN86
A	ASN109

site_id	AC6
Number of Residues	8
Details	binding site for residue PGE A 206

Chain	Residue
A	GLU17
A	ASN21
A	ARG79
A	PHE81
A	GLN83
A	HOH325
A	HOH447
B	LYS87

site_id	AC7
Number of Residues	9
Details	binding site for residue PEG A 207

Chain	Residue
A	HIS128
A	ASP131
A	PHE132
A	THR135
A	HIS136
A	HOH414
B	GLU134
B	ASN139
B	HOH366

site_id	AC8
Number of Residues	4
Details	binding site for residue PEG A 208

Chain	Residue
A	TYR40
A	ARG43
A	ASP45
A	ASP92

site_id	AC9
Number of Residues	4
Details	binding site for residue PEG A 209

Chain	Residue
A	TYR54
A	GLN58
A	GLU147
A	HOH405

site_id	AD1
Number of Residues	9
Details	binding site for residue PEG A 210

Chain	Residue
A	VAL8
A	ARG9
A	GLN10
A	GLN75
A	ARG76
A	HOH302
B	ASN111
B	VAL142
B	HOH331

site_id	AD2
Number of Residues	5
Details	binding site for residue PEG B 201

Chain	Residue
A	GLN7
B	ASP45
B	THR153
B	ARG156
B	HOH315

site_id	AD3
Number of Residues	7
Details	binding site for residue ZN B 202

Chain	Residue
B	GLU27
B	GLU62
B	HIS65
B	GLN141
B	ZN203
B	HOH301
B	HOH312

site_id	AD4
Number of Residues	5
Details	binding site for residue ZN B 203

Chain	Residue
B	GLU62
B	GLU107
B	ZN202
B	HOH301
B	HOH398

site_id	AD5
Number of Residues	8
Details	binding site for residue ZN B 204

Chain	Residue
B	HIS173
B	HIS173
B	HIS173
B	HIS173
B	HOH456
B	HOH456
B	HOH456
B	HOH456

site_id	AD6
Number of Residues	4
Details	binding site for residue ZN B 205

Chain	Residue
A	HIS122
B	HIS122
B	BYX207
F	HIS122

site_id	AD7
Number of Residues	2
Details	binding site for residue PEG B 206

Chain	Residue
B	TYR29
B	ASP89

site_id	AD8
Number of Residues	13
Details	binding site for residue BYX B 207

Chain	Residue
C	HIS122
C	ASP123
C	ZN201
D	HIS122
E	HIS122
F	HIS122
A	HIS122
A	ASP123
B	HIS122
B	ZN205
B	HOH351
B	HOH363
B	HOH404

site_id	AD9
Number of Residues	4
Details	binding site for residue ZN C 201

Chain	Residue
B	BYX207
C	HIS122
D	HIS122
E	HIS122

site_id	AE1
Number of Residues	6
Details	binding site for residue ZN C 202

Chain	Residue
C	GLU27
C	GLU62
C	HIS65
C	ZN203
C	HOH301
C	HOH309

site_id	AE2
Number of Residues	5
Details	binding site for residue ZN C 203

Chain	Residue
C	GLU62
C	GLU107
C	ZN202
C	HOH301
C	HOH352

site_id	AE3
Number of Residues	8
Details	binding site for residue ZN C 204

Chain	Residue
C	HIS173
C	HIS173
C	HIS173
C	HIS173
C	HOH435
C	HOH435
C	HOH435
C	HOH435

site_id	AE4
Number of Residues	6
Details	binding site for residue ZN C 205

Chain	Residue
C	ASP131
C	GLU134
D	ASP131
D	GLU134
E	ASP131
E	GLU134

site_id	AE5
Number of Residues	3
Details	binding site for residue PEG C 206

Chain	Residue
C	LYS71
C	HOH366
D	LYS49

site_id	AE6
Number of Residues	7
Details	binding site for residue PEG C 207

Chain	Residue
C	ASN11
C	ASN125
C	PRO127
E	GLN112
E	LEU115
E	HIS118
E	LYS119

site_id	AE7
Number of Residues	7
Details	binding site for residue PEG C 208

Chain	Residue
C	ASP42
C	LYS143
C	LYS146
C	GLU147
C	HOH320
D	LYS71
D	GLN75

site_id	AE8
Number of Residues	9
Details	binding site for residue PEG C 209

Chain	Residue
C	ALA47
C	HIS151
C	ASN154
C	TYR168
C	PHE170
C	ASP171
C	LYS172
C	THR174
C	HOH327

site_id	AE9
Number of Residues	5
Details	binding site for residue PEG C 210

Chain	Residue
C	ARG22
C	ASN25
C	LEU26
C	PEG211
C	HOH324

site_id	AF1
Number of Residues	4
Details	binding site for residue PEG C 211

Chain	Residue
C	ASN25
C	LEU26
C	TYR29
C	PEG210

site_id	AF2
Number of Residues	5
Details	binding site for residue ZN D 201

Chain	Residue
D	GLU62
D	GLU107
D	ZN202
D	HOH341
D	HOH436

site_id	AF3
Number of Residues	6
Details	binding site for residue ZN D 202

Chain	Residue
D	GLU27
D	GLU62
D	HIS65
D	ZN201
D	HOH319
D	HOH341

site_id	AF4
Number of Residues	8
Details	binding site for residue PGE D 203

Chain	Residue
D	ASN139
D	LYS143
D	LYS146
D	HOH301
D	HOH386
E	LYS71
E	GLN75
E	PEG203

site_id	AF5
Number of Residues	4
Details	binding site for residue PGE D 204

Chain	Residue
D	ARG9
D	ASN11
D	TYR12
D	HOH378

site_id	AF6
Number of Residues	3
Details	binding site for residue PGE D 205

Chain	Residue
D	LYS87
D	ASP89
D	GLU90

site_id	AF7
Number of Residues	4
Details	binding site for residue PEG D 206

Chain	Residue
D	TYR40
D	ARG43
D	ASP45
D	ASP92

site_id	AF8
Number of Residues	3
Details	binding site for residue PEG D 207

Chain	Residue
D	ASN25
D	LEU26
D	ASN109

site_id	AF9
Number of Residues	6
Details	binding site for residue ZN E 201

Chain	Residue
E	GLU27
E	GLU62
E	HIS65
E	GLN141
E	ZN202
E	HOH304

site_id	AG1
Number of Residues	3
Details	binding site for residue ZN E 202

Chain	Residue
E	GLU62
E	GLU107
E	ZN201

site_id	AG2
Number of Residues	8
Details	binding site for residue PEG E 203

Chain	Residue
D	ASN139
D	PGE203
E	LEU72
E	GLN75
E	HIS128
E	ASP131
E	PHE132
E	HOH309

site_id	AG3
Number of Residues	5
Details	binding site for residue PEG E 204

Chain	Residue
A	ASP15
A	ARG22
A	LEU120
A	HOH396
E	HOH374

site_id	AG4
Number of Residues	6
Details	binding site for residue ZN F 201

Chain	Residue
F	GLU27
F	GLU62
F	HIS65
F	GLN141
F	ZN202
F	HOH304

site_id	AG5
Number of Residues	4
Details	binding site for residue ZN F 202

Chain	Residue
F	GLU62
F	GLU107
F	ZN201
F	HOH428

site_id	AG6
Number of Residues	6
Details	binding site for residue PEG F 203

Chain	Residue
F	GLN86
F	HOH313
F	HOH317
F	HOH334
F	HOH357
F	HOH391

site_id	AG7
Number of Residues	2
Details	binding site for residue PEG F 204

Chain	Residue
A	LYS108
F	HOH311

site_id	AG8
Number of Residues	9
Details	binding site for residue PEG F 205

Chain	Residue
A	ASN111
A	VAL142
F	VAL8
F	ARG9
F	GLN10
F	TYR12
F	ARG76
F	HIS128
F	HOH320

Functional Information from PROSITE/UniProt

site_id	PS00204
Number of Residues	21
Details	FERRITIN_2 Ferritin iron-binding regions signature 2. DphLADFIEthYLneqvkaIK

Chain	Residue	Details
A	ASP126-LYS146

site_id	PS00540
Number of Residues	19
Details	FERRITIN_1 Ferritin iron-binding regions signature 1. EeREhaEKLMklQNqRgGR

Chain	Residue	Details
A	GLU61-ARG79

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	894
Details	Domain: {"description":"Ferritin-like diiron","evidences":[{"source":"PROSITE-ProRule","id":"PRU00085","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"1992356","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1FHA","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00085","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Site: {"description":"Essential for association with cargo receptor NCOA4","evidences":[{"source":"PubMed","id":"26436293","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)