Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5W4B

The crystal structure of human S-adenosylhomocysteine hydrolase (AHCY) bound to benzothiazole inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004013	molecular_function	adenosylhomocysteinase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005783	cellular_component	endoplasmic reticulum
A	0005829	cellular_component	cytosol
A	0006730	biological_process	one-carbon metabolic process
A	0016787	molecular_function	hydrolase activity
A	0033353	biological_process	S-adenosylmethionine cycle
A	0042470	cellular_component	melanosome
A	0070062	cellular_component	extracellular exosome
B	0004013	molecular_function	adenosylhomocysteinase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005783	cellular_component	endoplasmic reticulum
B	0005829	cellular_component	cytosol
B	0006730	biological_process	one-carbon metabolic process
B	0016787	molecular_function	hydrolase activity
B	0033353	biological_process	S-adenosylmethionine cycle
B	0042470	cellular_component	melanosome
B	0070062	cellular_component	extracellular exosome
C	0004013	molecular_function	adenosylhomocysteinase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005783	cellular_component	endoplasmic reticulum
C	0005829	cellular_component	cytosol
C	0006730	biological_process	one-carbon metabolic process
C	0016787	molecular_function	hydrolase activity
C	0033353	biological_process	S-adenosylmethionine cycle
C	0042470	cellular_component	melanosome
C	0070062	cellular_component	extracellular exosome
D	0004013	molecular_function	adenosylhomocysteinase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005783	cellular_component	endoplasmic reticulum
D	0005829	cellular_component	cytosol
D	0006730	biological_process	one-carbon metabolic process
D	0016787	molecular_function	hydrolase activity
D	0033353	biological_process	S-adenosylmethionine cycle
D	0042470	cellular_component	melanosome
D	0070062	cellular_component	extracellular exosome
E	0004013	molecular_function	adenosylhomocysteinase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005783	cellular_component	endoplasmic reticulum
E	0005829	cellular_component	cytosol
E	0006730	biological_process	one-carbon metabolic process
E	0016787	molecular_function	hydrolase activity
E	0033353	biological_process	S-adenosylmethionine cycle
E	0042470	cellular_component	melanosome
E	0070062	cellular_component	extracellular exosome
F	0004013	molecular_function	adenosylhomocysteinase activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005783	cellular_component	endoplasmic reticulum
F	0005829	cellular_component	cytosol
F	0006730	biological_process	one-carbon metabolic process
F	0016787	molecular_function	hydrolase activity
F	0033353	biological_process	S-adenosylmethionine cycle
F	0042470	cellular_component	melanosome
F	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	27
Details	binding site for residue NAD A 501

Chain	Residue
A	ASP190
A	ASN248
A	THR275
A	THR276
A	GLY277
A	CYS278
A	ILE281
A	ILE299
A	GLY300
A	HIS301
A	LEU344
A	ASN191
A	ASN346
A	HOH611
A	HOH634
A	HOH649
A	HOH682
B	GLN413
B	LYS426
B	TYR430
A	GLY222
A	ASP223
A	VAL224
A	THR242
A	GLU243
A	ILE244
A	ASP245

site_id	AC2
Number of Residues	10
Details	binding site for residue 9W4 A 502

Chain	Residue
A	HIS55
A	THR57
A	GLU59
A	ASN80
A	GLN324
A	ARG343
A	LEU347
A	HIS353
A	MET358
A	HOH645

site_id	AC3
Number of Residues	30
Details	binding site for residue NAD B 501

Chain	Residue
A	GLN413
A	LYS426
A	TYR430
B	ASP190
B	ASN191
B	GLY222
B	ASP223
B	VAL224
B	THR242
B	GLU243
B	ILE244
B	ASP245
B	ASN248
B	THR275
B	THR276
B	GLY277
B	CYS278
B	ILE281
B	ILE299
B	GLY300
B	HIS301
B	LEU344
B	ASN346
B	HOH616
B	HOH631
B	HOH652
B	HOH664
B	HOH684
B	HOH695
B	HOH706

site_id	AC4
Number of Residues	12
Details	binding site for residue 9W4 B 502

Chain	Residue
B	HIS55
B	THR57
B	GLU59
B	ASN80
B	PHE82
B	SER83
B	GLN324
B	ARG343
B	LEU347
B	HIS353
B	MET358
B	HOH611

site_id	AC5
Number of Residues	29
Details	binding site for residue NAD C 501

Chain	Residue
C	HOH644
C	HOH651
C	HOH656
C	HOH673
C	HOH681
C	HOH685
D	GLN413
D	LYS426
D	TYR430
C	ASP190
C	ASN191
C	GLY222
C	ASP223
C	VAL224
C	THR242
C	GLU243
C	ILE244
C	ASP245
C	ASN248
C	THR275
C	THR276
C	GLY277
C	CYS278
C	ILE281
C	ILE299
C	GLY300
C	HIS301
C	ASN346
C	HOH601

site_id	AC6
Number of Residues	8
Details	binding site for residue 9W4 C 502

Chain	Residue
C	HIS55
C	THR57
C	GLU59
C	ASN80
C	ARG343
C	LEU347
C	HIS353
C	MET358

site_id	AC7
Number of Residues	29
Details	binding site for residue NAD D 501

Chain	Residue
C	GLN413
C	LYS426
C	TYR430
D	ASP190
D	ASN191
D	GLY222
D	ASP223
D	VAL224
D	THR242
D	GLU243
D	ILE244
D	ASP245
D	ASN248
D	THR275
D	THR276
D	GLY277
D	CYS278
D	ILE281
D	ILE299
D	GLY300
D	HIS301
D	ASN346
D	HOH608
D	HOH644
D	HOH658
D	HOH682
D	HOH691
D	HOH718
D	HOH734

site_id	AC8
Number of Residues	10
Details	binding site for residue 9W4 D 502

Chain	Residue
D	HIS55
D	THR57
D	GLU59
D	ASN80
D	PHE82
D	GLN324
D	ARG343
D	LEU347
D	HIS353
D	MET358

site_id	AC9
Number of Residues	29
Details	binding site for residue NAD E 501

Chain	Residue
E	ASP190
E	ASN191
E	GLY222
E	ASP223
E	VAL224
E	THR242
E	GLU243
E	ILE244
E	ASP245
E	ASN248
E	THR275
E	THR276
E	GLY277
E	CYS278
E	ILE281
E	ILE299
E	GLY300
E	HIS301
E	LEU344
E	ASN346
E	HOH619
E	HOH623
E	HOH651
E	HOH673
E	HOH684
E	HOH685
F	GLN413
F	LYS426
F	TYR430

site_id	AD1
Number of Residues	13
Details	binding site for residue 9W4 E 502

Chain	Residue
E	HIS55
E	THR57
E	GLU59
E	ASN80
E	SER83
E	GLN324
E	ARG343
E	LEU347
E	HIS353
E	MET358
E	EDO503
E	HOH696
E	HOH732

site_id	AD2
Number of Residues	4
Details	binding site for residue EDO E 503

Chain	Residue
E	ARG343
E	LEU344
E	9W4502
E	HOH620

site_id	AD3
Number of Residues	29
Details	binding site for residue NAD F 501

Chain	Residue
E	GLN413
E	LYS426
E	TYR430
F	ASP190
F	ASN191
F	GLY222
F	ASP223
F	VAL224
F	GLU243
F	ILE244
F	ASP245
F	ASN248
F	THR275
F	THR276
F	GLY277
F	CYS278
F	ILE281
F	ILE299
F	GLY300
F	HIS301
F	ASN346
F	HIS353
F	HOH656
F	HOH675
F	HOH677
F	HOH696
F	HOH703
F	HOH714
F	HOH724

site_id	AD4
Number of Residues	14
Details	binding site for residue 9W4 F 502

Chain	Residue
F	HIS55
F	THR57
F	GLU59
F	ASN80
F	PHE82
F	SER83
F	GLN324
F	ARG343
F	LEU347
F	MET351
F	HIS353
F	MET358
F	HOH640
F	HOH644

Functional Information from PROSITE/UniProt

site_id	PS00738
Number of Residues	15
Details	ADOHCYASE_1 S-adenosyl-L-homocysteine hydrolase signature 1. SCNiFSTQDhAAAAI

Chain	Residue	Details
A	SER78-ILE92

site_id	PS00739
Number of Residues	17
Details	ADOHCYASE_2 S-adenosyl-L-homocysteine hydrolase signature 2. GKvavVaGYGdVGKGc.A

Chain	Residue	Details
A	GLY213-ALA229

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	30
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P10760

Chain	Residue	Details
D	LYS186
D	ASP190
E	THR57
E	ASP131
E	GLU156
E	LYS186
E	ASP190
F	THR57
F	ASP131
F	GLU156
F	LYS186
F	ASP190
A	THR57
A	ASP131
A	GLU156
A	LYS186
A	ASP190
B	THR57
B	ASP131
B	GLU156
B	LYS186
B	ASP190
C	THR57
C	ASP131
C	GLU156
C	LYS186
C	ASP190
D	THR57
D	ASP131
D	GLU156

site_id	SWS_FT_FI2
Number of Residues	42
Details	BINDING: BINDING => ECO:0000269\|PubMed:12590576, ECO:0000269\|PubMed:9586999

Chain	Residue	Details
E	GLU243
E	ASN248
E	ILE299
E	ASN346
E	HIS353
F	THR157
F	GLY222
F	GLU243
F	ASN248
F	ILE299
F	ASN346
F	HIS353
A	THR157
A	GLY222
A	GLU243
A	ASN248
A	ILE299
D	GLY222
D	GLU243
D	ASN248
D	ILE299
D	ASN346
D	HIS353
E	THR157
E	GLY222
A	ASN346
A	HIS353
B	THR157
B	GLY222
B	GLU243
B	ASN248
B	ILE299
B	ASN346
B	HIS353
C	THR157
C	GLY222
C	GLU243
C	ASN248
C	ILE299
C	ASN346
C	HIS353
D	THR157

site_id	SWS_FT_FI3
Number of Residues	6
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER183
B	SER183
C	SER183
D	SER183
E	SER183
F	SER183

site_id	SWS_FT_FI4
Number of Residues	6
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269\|PubMed:29192674

Chain	Residue	Details
A	LYS186
D	LYS186
E	LYS186
F	LYS186
B	LYS186
C	LYS186

site_id	SWS_FT_FI5
Number of Residues	6
Details	MOD_RES: Phosphotyrosine => ECO:0000250\|UniProtKB:P50247

Chain	Residue	Details
A	TYR193
D	TYR193
E	TYR193
F	TYR193
B	TYR193
C	TYR193

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