Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7ERB

Crystal structure of human Biliverdin IX-beta reductase B with Ataluren (PTC)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004074	molecular_function	biliverdin reductase (NAD(P)H) activity
A	0005515	molecular_function	protein binding
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0008752	molecular_function	FMN reductase (NAD(P)H) activity
A	0016491	molecular_function	oxidoreductase activity
A	0016740	molecular_function	transferase activity
A	0030219	biological_process	megakaryocyte differentiation
A	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
A	0042167	biological_process	heme catabolic process
A	0042602	molecular_function	riboflavin reductase (NADPH) activity
A	0043231	cellular_component	intracellular membrane-bounded organelle
A	0046627	biological_process	negative regulation of insulin receptor signaling pathway
A	0052873	molecular_function	FMN reductase (NADPH) activity
A	0052874	molecular_function	FMN reductase (NADH) activity
A	0070062	cellular_component	extracellular exosome
A	0106276	molecular_function	biliberdin reductase NAD+ activity
A	0106277	molecular_function	biliverdin reductase (NADPH) activity
B	0004074	molecular_function	biliverdin reductase (NAD(P)H) activity
B	0005515	molecular_function	protein binding
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0008752	molecular_function	FMN reductase (NAD(P)H) activity
B	0016491	molecular_function	oxidoreductase activity
B	0016740	molecular_function	transferase activity
B	0030219	biological_process	megakaryocyte differentiation
B	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
B	0042167	biological_process	heme catabolic process
B	0042602	molecular_function	riboflavin reductase (NADPH) activity
B	0043231	cellular_component	intracellular membrane-bounded organelle
B	0046627	biological_process	negative regulation of insulin receptor signaling pathway
B	0052873	molecular_function	FMN reductase (NADPH) activity
B	0052874	molecular_function	FMN reductase (NADH) activity
B	0070062	cellular_component	extracellular exosome
B	0106276	molecular_function	biliberdin reductase NAD+ activity
B	0106277	molecular_function	biliverdin reductase (NADPH) activity
C	0004074	molecular_function	biliverdin reductase (NAD(P)H) activity
C	0005515	molecular_function	protein binding
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0008752	molecular_function	FMN reductase (NAD(P)H) activity
C	0016491	molecular_function	oxidoreductase activity
C	0016740	molecular_function	transferase activity
C	0030219	biological_process	megakaryocyte differentiation
C	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
C	0042167	biological_process	heme catabolic process
C	0042602	molecular_function	riboflavin reductase (NADPH) activity
C	0043231	cellular_component	intracellular membrane-bounded organelle
C	0046627	biological_process	negative regulation of insulin receptor signaling pathway
C	0052873	molecular_function	FMN reductase (NADPH) activity
C	0052874	molecular_function	FMN reductase (NADH) activity
C	0070062	cellular_component	extracellular exosome
C	0106276	molecular_function	biliberdin reductase NAD+ activity
C	0106277	molecular_function	biliverdin reductase (NADPH) activity
D	0004074	molecular_function	biliverdin reductase (NAD(P)H) activity
D	0005515	molecular_function	protein binding
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0008752	molecular_function	FMN reductase (NAD(P)H) activity
D	0016491	molecular_function	oxidoreductase activity
D	0016740	molecular_function	transferase activity
D	0030219	biological_process	megakaryocyte differentiation
D	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
D	0042167	biological_process	heme catabolic process
D	0042602	molecular_function	riboflavin reductase (NADPH) activity
D	0043231	cellular_component	intracellular membrane-bounded organelle
D	0046627	biological_process	negative regulation of insulin receptor signaling pathway
D	0052873	molecular_function	FMN reductase (NADPH) activity
D	0052874	molecular_function	FMN reductase (NADH) activity
D	0070062	cellular_component	extracellular exosome
D	0106276	molecular_function	biliberdin reductase NAD+ activity
D	0106277	molecular_function	biliverdin reductase (NADPH) activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	36
Details	binding site for residue NAP A 401

Chain	Residue
A	GLY10
A	LEU74
A	LEU75
A	GLY76
A	ARG78
A	VAL86
A	MET87
A	CYS109
A	THR110
A	HIS132
A	PRO151
A	THR12
A	PRO152
A	HIS153
A	ILE154
A	JBF402
A	HOH523
A	HOH532
A	HOH547
A	HOH565
A	HOH583
A	HOH590
A	GLY13
A	HOH606
A	HOH608
A	HOH625
A	HOH663
D	SER82
D	HOH540
D	HOH613
A	GLN14
A	THR15
A	ARG35
A	SER38
A	ASP54
A	VAL55

site_id	AC2
Number of Residues	11
Details	binding site for residue JBF A 402

Chain	Residue
A	ARG78
A	SER111
A	PHE113
A	TRP116
A	PRO152
A	HIS153
A	ARG174
A	NAP401
A	HOH554
A	HOH607
A	HOH672

site_id	AC3
Number of Residues	11
Details	binding site for residue JBF A 403

Chain	Residue
A	ASP130
A	ARG134
A	HOH516
B	SER111
B	PHE113
B	PRO152
B	HIS153
B	ARG174
B	NAP401
B	HOH521
B	HOH525

site_id	AC4
Number of Residues	4
Details	binding site for residue SO4 A 404

Chain	Residue
A	ARG174
A	HOH652
C	MET1
C	ALA2

site_id	AC5
Number of Residues	2
Details	binding site for residue SO4 A 405

Chain	Residue
A	ARG46
A	HOH537

site_id	AC6
Number of Residues	33
Details	binding site for residue NAP B 401

Chain	Residue
A	JBF403
B	GLY10
B	THR12
B	GLY13
B	GLN14
B	THR15
B	ARG35
B	ARG39
B	ASP54
B	VAL55
B	LEU74
B	LEU75
B	GLY76
B	ARG78
B	MET87
B	CYS109
B	THR110
B	SER111
B	HIS132
B	PRO151
B	PRO152
B	ILE154
B	HOH507
B	HOH525
B	HOH531
B	HOH539
B	HOH558
B	HOH565
B	HOH580
B	HOH586
B	HOH596
B	HOH598
C	SER37

site_id	AC7
Number of Residues	10
Details	binding site for residue SO4 B 402

Chain	Residue
A	HOH567
B	HIS153
B	GLY155
B	ASP156
B	GLN157
B	VAL175
B	HOH588
B	HOH628
A	LYS137
A	ARG140

site_id	AC8
Number of Residues	37
Details	binding site for residue NAP C 401

Chain	Residue
B	SER82
B	HOH562
B	HOH613
C	GLY10
C	THR12
C	GLY13
C	GLN14
C	THR15
C	ARG35
C	SER38
C	ASP54
C	VAL55
C	LEU74
C	LEU75
C	GLY76
C	THR77
C	ARG78
C	VAL86
C	MET87
C	CYS109
C	THR110
C	HIS132
C	PRO151
C	PRO152
C	HIS153
C	ILE154
C	JBF402
C	HOH540
C	HOH544
C	HOH552
C	HOH555
C	HOH574
C	HOH591
C	HOH597
C	HOH623
C	HOH635
C	HOH653

site_id	AC9
Number of Residues	12
Details	binding site for residue JBF C 402

Chain	Residue
C	ARG78
C	SER111
C	PHE113
C	TRP116
C	PRO152
C	HIS153
C	ARG174
C	NAP401
C	HOH545
C	HOH572
C	HOH619
C	HOH661

site_id	AD1
Number of Residues	10
Details	binding site for residue JBF C 403

Chain	Residue
C	ASP130
C	ARG134
C	HOH521
D	ARG78
D	SER111
D	PHE113
D	HIS153
D	ARG174
D	NAP401
D	HOH515

site_id	AD2
Number of Residues	4
Details	binding site for residue SO4 C 404

Chain	Residue
A	ALA2
C	ARG174
C	HOH514
C	HOH524

site_id	AD3
Number of Residues	4
Details	binding site for residue SO4 C 405

Chain	Residue
C	HIS183
C	HOH669
D	ALA2
D	LYS4

site_id	AD4
Number of Residues	37
Details	binding site for residue NAP D 401

Chain	Residue
A	SER37
C	JBF403
D	GLY10
D	THR12
D	GLY13
D	GLN14
D	THR15
D	ARG35
D	ARG39
D	ASP54
D	VAL55
D	LEU74
D	LEU75
D	GLY76
D	ARG78
D	MET87
D	CYS109
D	THR110
D	SER111
D	HIS132
D	PRO151
D	PRO152
D	ILE154
D	HOH515
D	HOH531
D	HOH552
D	HOH558
D	HOH563
D	HOH565
D	HOH573
D	HOH574
D	HOH580
D	HOH587
D	HOH589
D	HOH596
D	HOH598
D	HOH631

site_id	AD5
Number of Residues	8
Details	binding site for residue SO4 D 402

Chain	Residue
C	LYS137
C	ARG140
D	HIS153
D	GLY155
D	ASP156
D	GLN157
D	HOH590
D	HOH607

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: S-nitroso-cysteine intermediate; for S-nitroso-CoA-dependent nitrosyltransferase activity => ECO:0000269\|PubMed:38056462

Chain	Residue	Details
A	CYS109
A	CYS188
B	CYS109
B	CYS188
C	CYS109
C	CYS188
D	CYS109
D	CYS188

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:11224564, ECO:0000269\|PubMed:29487133, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:1HDO, ECO:0007744\|PDB:5OOG, ECO:0007744\|PDB:5OOH, ECO:0007744\|PDB:7ER7

Chain	Residue	Details
C	GLY10
D	GLY10
A	GLY10
B	GLY10

site_id	SWS_FT_FI3
Number of Residues	32
Details	BINDING: BINDING => ECO:0000269\|PubMed:11224564, ECO:0000269\|PubMed:29487133, ECO:0000269\|PubMed:32246827, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:1HDO, ECO:0007744\|PDB:1HE2, ECO:0007744\|PDB:1HE3, ECO:0007744\|PDB:1HE4, ECO:0007744\|PDB:1HE5, ECO:0007744\|PDB:5OOG, ECO:0007744\|PDB:5OOH, ECO:0007744\|PDB:6OPL, ECO:0007744\|PDB:7ER6, ECO:0007744\|PDB:7ER7, ECO:0007744\|PDB:7ER8, ECO:0007744\|PDB:7ER9, ECO:0007744\|PDB:7ERA, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERC, ECO:0007744\|PDB:7ERD, ECO:0007744\|PDB:7ERE

Chain	Residue	Details
B	THR15
B	ARG35
B	ASP54
B	VAL55
B	GLY76
B	ARG78
B	MET87
C	THR12
C	THR15
C	ARG35
C	ASP54
C	VAL55
C	GLY76
C	ARG78
C	MET87
D	THR12
D	THR15
D	ARG35
D	ASP54
D	VAL55
D	GLY76
D	ARG78
D	MET87
A	VAL55
A	GLY76
A	ARG78
A	MET87
B	THR12
A	THR15
A	ARG35
A	ASP54
A	THR12

site_id	SWS_FT_FI4
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:11224564, ECO:0000269\|PubMed:32246827, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:1HDO, ECO:0007744\|PDB:1HE2, ECO:0007744\|PDB:1HE3, ECO:0007744\|PDB:1HE4, ECO:0007744\|PDB:1HE5, ECO:0007744\|PDB:5OOG, ECO:0007744\|PDB:5OOH, ECO:0007744\|PDB:6OPL, ECO:0007744\|PDB:7ER6, ECO:0007744\|PDB:7ER7, ECO:0007744\|PDB:7ER8, ECO:0007744\|PDB:7ER9, ECO:0007744\|PDB:7ERA, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERC, ECO:0007744\|PDB:7ERD, ECO:0007744\|PDB:7ERE

Chain	Residue	Details
A	GLY13
B	GLY13
C	GLY13
D	GLY13

site_id	SWS_FT_FI5
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:11224564, ECO:0000269\|PubMed:29487133, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:1HDO, ECO:0007744\|PDB:1HE2, ECO:0007744\|PDB:1HE3, ECO:0007744\|PDB:1HE4, ECO:0007744\|PDB:1HE5, ECO:0007744\|PDB:5OOG, ECO:0007744\|PDB:5OOH, ECO:0007744\|PDB:7ER6, ECO:0007744\|PDB:7ER7, ECO:0007744\|PDB:7ER8, ECO:0007744\|PDB:7ER9, ECO:0007744\|PDB:7ERA, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERC, ECO:0007744\|PDB:7ERD, ECO:0007744\|PDB:7ERE

Chain	Residue	Details
A	GLN14
A	ILE154
B	GLN14
B	ILE154
C	GLN14
C	ILE154
D	GLN14
D	ILE154

site_id	SWS_FT_FI6
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:7ER6, ECO:0007744\|PDB:7ER9, ECO:0007744\|PDB:7ERA, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERD, ECO:0007744\|PDB:7ERE

Chain	Residue	Details
A	SER38
B	SER38
C	SER38
D	SER38

site_id	SWS_FT_FI7
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:29487133, ECO:0000269\|PubMed:32246827, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:5OOH, ECO:0007744\|PDB:6OPL, ECO:0007744\|PDB:7ER6, ECO:0007744\|PDB:7ER7, ECO:0007744\|PDB:7ER8, ECO:0007744\|PDB:7ER9, ECO:0007744\|PDB:7ERA, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERC, ECO:0007744\|PDB:7ERE

Chain	Residue	Details
A	ARG39
B	ARG39
C	ARG39
D	ARG39

site_id	SWS_FT_FI8
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:11224564, ECO:0000269\|PubMed:32246827, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:1HDO, ECO:0007744\|PDB:1HE2, ECO:0007744\|PDB:1HE3, ECO:0007744\|PDB:1HE4, ECO:0007744\|PDB:1HE5, ECO:0007744\|PDB:6OPL, ECO:0007744\|PDB:7ER6, ECO:0007744\|PDB:7ER7, ECO:0007744\|PDB:7ER8, ECO:0007744\|PDB:7ER9, ECO:0007744\|PDB:7ERA, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERC, ECO:0007744\|PDB:7ERD, ECO:0007744\|PDB:7ERE

Chain	Residue	Details
A	LEU75
B	LEU75
C	LEU75
D	LEU75

site_id	SWS_FT_FI9
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:11224564, ECO:0000269\|PubMed:29487133, ECO:0000269\|PubMed:32246827, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:1HDO, ECO:0007744\|PDB:1HE2, ECO:0007744\|PDB:1HE3, ECO:0007744\|PDB:1HE4, ECO:0007744\|PDB:1HE5, ECO:0007744\|PDB:5OOH, ECO:0007744\|PDB:6OPL, ECO:0007744\|PDB:7ER6, ECO:0007744\|PDB:7ER7, ECO:0007744\|PDB:7ER8, ECO:0007744\|PDB:7ER9, ECO:0007744\|PDB:7ERA, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERC, ECO:0007744\|PDB:7ERD, ECO:0007744\|PDB:7ERE

Chain	Residue	Details
A	CYS109
B	CYS109
C	CYS109
D	CYS109

site_id	SWS_FT_FI10
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:11224564, ECO:0000269\|PubMed:29487133, ECO:0000269\|PubMed:32246827, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:1HE3, ECO:0007744\|PDB:5OOG, ECO:0007744\|PDB:5OOH, ECO:0007744\|PDB:6OPL, ECO:0007744\|PDB:7ER8, ECO:0007744\|PDB:7ER9, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERC

Chain	Residue	Details
A	HIS132
B	HIS132
C	HIS132
D	HIS132

site_id	SWS_FT_FI11
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:32246827, ECO:0000269\|PubMed:34957824, ECO:0007744\|PDB:6OPL, ECO:0007744\|PDB:7ERB, ECO:0007744\|PDB:7ERD

Chain	Residue	Details
A	HIS153
B	HIS153
C	HIS153
D	HIS153

site_id	SWS_FT_FI12
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:24275569

Chain	Residue	Details
A	SER42
B	SER42
C	SER42
D	SER42

site_id	SWS_FT_FI13
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER82
B	SER82
C	SER82
D	SER82

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