6NBD

Human methemoglobin state 2 determined using single-particle cryo-EM at 200 keV

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004601	molecular_function	peroxidase activity
A	0005344	molecular_function	oxygen carrier activity
A	0005506	molecular_function	iron ion binding
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005615	cellular_component	extracellular space
A	0005829	cellular_component	cytosol
A	0005833	cellular_component	hemoglobin complex
A	0015670	biological_process	carbon dioxide transport
A	0015671	biological_process	oxygen transport
A	0016020	cellular_component	membrane
A	0019825	molecular_function	oxygen binding
A	0020037	molecular_function	heme binding
A	0030185	biological_process	nitric oxide transport
A	0031720	molecular_function	haptoglobin binding
A	0031838	cellular_component	haptoglobin-hemoglobin complex
A	0042542	biological_process	response to hydrogen peroxide
A	0042744	biological_process	hydrogen peroxide catabolic process
A	0043177	molecular_function	organic acid binding
A	0046872	molecular_function	metal ion binding
A	0070062	cellular_component	extracellular exosome
A	0071682	cellular_component	endocytic vesicle lumen
A	0072562	cellular_component	blood microparticle
A	0098869	biological_process	cellular oxidant detoxification
B	0004601	molecular_function	peroxidase activity
B	0005344	molecular_function	oxygen carrier activity
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005615	cellular_component	extracellular space
B	0005829	cellular_component	cytosol
B	0005833	cellular_component	hemoglobin complex
B	0008217	biological_process	regulation of blood pressure
B	0015670	biological_process	carbon dioxide transport
B	0015671	biological_process	oxygen transport
B	0019825	molecular_function	oxygen binding
B	0020037	molecular_function	heme binding
B	0030185	biological_process	nitric oxide transport
B	0030492	molecular_function	hemoglobin binding
B	0031720	molecular_function	haptoglobin binding
B	0031721	molecular_function	hemoglobin alpha binding
B	0031838	cellular_component	haptoglobin-hemoglobin complex
B	0042542	biological_process	response to hydrogen peroxide
B	0042744	biological_process	hydrogen peroxide catabolic process
B	0043177	molecular_function	organic acid binding
B	0045429	biological_process	positive regulation of nitric oxide biosynthetic process
B	0046872	molecular_function	metal ion binding
B	0070062	cellular_component	extracellular exosome
B	0070293	biological_process	renal absorption
B	0070527	biological_process	platelet aggregation
B	0071682	cellular_component	endocytic vesicle lumen
B	0072562	cellular_component	blood microparticle
B	0097746	biological_process	blood vessel diameter maintenance
B	0098869	biological_process	cellular oxidant detoxification
B	1904724	cellular_component	tertiary granule lumen
B	1904813	cellular_component	ficolin-1-rich granule lumen
C	0004601	molecular_function	peroxidase activity
C	0005344	molecular_function	oxygen carrier activity
C	0005506	molecular_function	iron ion binding
C	0005515	molecular_function	protein binding
C	0005576	cellular_component	extracellular region
C	0005615	cellular_component	extracellular space
C	0005829	cellular_component	cytosol
C	0005833	cellular_component	hemoglobin complex
C	0015670	biological_process	carbon dioxide transport
C	0015671	biological_process	oxygen transport
C	0016020	cellular_component	membrane
C	0019825	molecular_function	oxygen binding
C	0020037	molecular_function	heme binding
C	0030185	biological_process	nitric oxide transport
C	0031720	molecular_function	haptoglobin binding
C	0031838	cellular_component	haptoglobin-hemoglobin complex
C	0042542	biological_process	response to hydrogen peroxide
C	0042744	biological_process	hydrogen peroxide catabolic process
C	0043177	molecular_function	organic acid binding
C	0046872	molecular_function	metal ion binding
C	0070062	cellular_component	extracellular exosome
C	0071682	cellular_component	endocytic vesicle lumen
C	0072562	cellular_component	blood microparticle
C	0098869	biological_process	cellular oxidant detoxification
D	0004601	molecular_function	peroxidase activity
D	0005344	molecular_function	oxygen carrier activity
D	0005515	molecular_function	protein binding
D	0005576	cellular_component	extracellular region
D	0005615	cellular_component	extracellular space
D	0005829	cellular_component	cytosol
D	0005833	cellular_component	hemoglobin complex
D	0008217	biological_process	regulation of blood pressure
D	0015670	biological_process	carbon dioxide transport
D	0015671	biological_process	oxygen transport
D	0019825	molecular_function	oxygen binding
D	0020037	molecular_function	heme binding
D	0030185	biological_process	nitric oxide transport
D	0030492	molecular_function	hemoglobin binding
D	0031720	molecular_function	haptoglobin binding
D	0031721	molecular_function	hemoglobin alpha binding
D	0031838	cellular_component	haptoglobin-hemoglobin complex
D	0042542	biological_process	response to hydrogen peroxide
D	0042744	biological_process	hydrogen peroxide catabolic process
D	0043177	molecular_function	organic acid binding
D	0045429	biological_process	positive regulation of nitric oxide biosynthetic process
D	0046872	molecular_function	metal ion binding
D	0070062	cellular_component	extracellular exosome
D	0070293	biological_process	renal absorption
D	0070527	biological_process	platelet aggregation
D	0071682	cellular_component	endocytic vesicle lumen
D	0072562	cellular_component	blood microparticle
D	0097746	biological_process	blood vessel diameter maintenance
D	0098869	biological_process	cellular oxidant detoxification
D	1904724	cellular_component	tertiary granule lumen
D	1904813	cellular_component	ficolin-1-rich granule lumen

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	binding site for residue HEM A 201

Chain	Residue
A	TYR42
A	ASN97
A	PHE98
A	LEU101
A	LEU136
A	PHE43
A	HIS45
A	PHE46
A	HIS58
A	LYS61
A	LEU83
A	HIS87
A	LEU91

---

site_id	AC2
Number of Residues	12
Details	binding site for residue HEM B 201

Chain	Residue
B	THR38
B	PHE41
B	PHE42
B	HIS63
B	LYS66
B	ALA70
B	HIS92
B	LEU96
B	ASN102
B	PHE103
B	LEU106
B	LEU141

---

site_id	AC3
Number of Residues	15
Details	binding site for residue HEM C 201

Chain	Residue
C	TYR42
C	PHE43
C	HIS45
C	PHE46
C	HIS58
C	LYS61
C	LEU83
C	LEU86
C	HIS87
C	LEU91
C	ASN97
C	PHE98
C	LEU101
C	VAL132
C	LEU136

---

site_id	AC4
Number of Residues	14
Details	binding site for residue HEM D 201

Chain	Residue
D	THR38
D	PHE41
D	PHE42
D	HIS63
D	LYS66
D	ALA70
D	PHE71
D	HIS92
D	LEU96
D	ASN102
D	PHE103
D	LEU106
D	VAL137
D	LEU141

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	BINDING:

Chain	Residue	Details
B	VAL1
B	HIS2
B	LYS82
B	HIS143
D	VAL1
D	HIS2
D	LYS82
D	HIS143

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	BINDING: distal binding residue

Chain	Residue	Details
B	HIS63
D	HIS63

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	BINDING: proximal binding residue

Chain	Residue	Details
B	HIS92
A	LEU91
A	LEU106
A	THR108
A	VAL121
A	SER133
C	THR8
C	ALA13
C	TYR24
C	LEU29
C	HIS45
D	HIS92
C	ASP47
C	SER52
C	VAL55
C	GLY59
C	LEU91
C	LEU106
C	THR108
C	VAL121
C	SER133
A	TYR24
A	LEU29
A	HIS45
A	ASP47
A	SER52
A	VAL55
A	GLY59

---

site_id	SWS_FT_FI4
Number of Residues	36
Details	SITE: (Microbial infection) Cleavage; by N.americanus apr-2 => ECO:0000269|PubMed:12552433

Chain	Residue	Details
B	GLU7
B	GLY74
B	THR84
B	HIS92
B	ARG104
B	LEU110
B	GLY119
B	PHE122
B	ALA128
B	ALA140
D	GLU7
B	GLY25
D	GLY25
D	GLY29
D	TYR35
D	TRP37
D	PHE45
D	ASP52
D	GLY56
D	PHE71
D	GLY74
D	THR84
B	GLY29
D	HIS92
D	ARG104
D	LEU110
D	GLY119
D	PHE122
D	ALA128
D	ALA140
B	TYR35
B	TRP37
B	PHE45
B	ASP52
B	GLY56
B	PHE71

---

site_id	SWS_FT_FI5
Number of Residues	6
Details	SITE: Not glycated => ECO:0000269|PubMed:7358733

Chain	Residue	Details
B	LYS59
B	LYS82
B	LYS95
D	LYS59
D	LYS82
D	LYS95

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N-pyruvate 2-iminyl-valine; in Hb A1b

Chain	Residue	Details
B	VAL1
D	VAL1
A	LYS40
C	LYS7
C	LYS16
C	LYS40

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
B	SER9
B	SER44
D	SER9
D	SER44

---

site_id	SWS_FT_FI8
Number of Residues	6
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
B	THR12
B	THR50
B	THR87
D	THR12
D	THR50
D	THR87

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:4531009

Chain	Residue	Details
B	LYS59
B	LYS82
D	LYS59
D	LYS82

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:8637569, ECO:0000269|PubMed:9843411

Chain	Residue	Details
B	CYS93
D	CYS93
A	SER131
A	SER138
C	SER102
C	SER124
C	SER131
C	SER138

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	CARBOHYD: N-linked (Glc) (glycation) valine; in Hb A1c => ECO:0000269|PubMed:635569

Chain	Residue	Details
B	VAL1
D	VAL1
A	THR137
C	THR108
C	THR134
C	THR137

---

site_id	SWS_FT_FI12
Number of Residues	8
Details	CARBOHYD: N-linked (Glc) (glycation) lysine => ECO:0000269|PubMed:7358733

Chain	Residue	Details
B	LYS8
B	LYS17
B	LYS66
B	LYS120
D	LYS8
D	LYS17
D	LYS66
D	LYS120

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	CARBOHYD: N-linked (Glc) (glycation) lysine => ECO:0000269|PubMed:7358733

Chain	Residue	Details
A	LYS61
C	LYS61

---