Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4LVC

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004013	molecular_function	adenosylhomocysteinase activity
A	0005737	cellular_component	cytoplasm
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	0071269	biological_process	L-homocysteine biosynthetic process
B	0004013	molecular_function	adenosylhomocysteinase activity
B	0005737	cellular_component	cytoplasm
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	0071269	biological_process	L-homocysteine biosynthetic process
C	0004013	molecular_function	adenosylhomocysteinase activity
C	0005737	cellular_component	cytoplasm
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	0071269	biological_process	L-homocysteine biosynthetic process
D	0004013	molecular_function	adenosylhomocysteinase activity
D	0005737	cellular_component	cytoplasm
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	0071269	biological_process	L-homocysteine biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	BINDING SITE FOR RESIDUE ADN A 501

Chain	Residue
A	LEU57
A	ASP231
A	HIS342
A	LEU383
A	MET390
A	GLY391
A	HIS392
A	MET397
A	PHE401
A	NAD503
A	HIS58
A	THR60
A	GLN62
A	THR63
A	ASP135
A	GLU197
A	THR198
A	LYS227

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NH4 A 502

Chain	Residue
A	GLN62
A	MET390
A	HIS392
A	HOH717
A	HOH763
C	HOH620

site_id	AC3
Number of Residues	31
Details	BINDING SITE FOR RESIDUE NAD A 503

Chain	Residue
A	THR198
A	THR199
A	THR200
A	ASN232
A	GLY263
A	ASP264
A	VAL265
A	GLU284
A	VAL285
A	ASP286
A	CYS289
A	THR317
A	GLY318
A	ASN319
A	ILE322
A	ILE340
A	GLY341
A	HIS342
A	LEU383
A	ASN385
A	HIS392
A	ADN501
A	HOH604
A	HOH626
A	HOH641
A	HOH719
A	HOH787
A	HOH813
B	GLN454
B	LYS467
B	TYR471

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 504

Chain	Residue
A	THR200
A	HIS203
A	GLY318
A	HOH786
A	HOH1009
B	TYR457

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 505

Chain	Residue
A	LEU427
A	LYS429
A	ASP432
A	ASP469
B	ARG472

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 506

Chain	Residue
A	LYS106
A	ARG246
A	GLY387
A	ASN388
A	ALA389
A	HOH1026

site_id	AC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ADN B 501

Chain	Residue
B	HIS58
B	THR60
B	GLN62
B	THR63
B	ASP135
B	GLU197
B	THR198
B	LYS227
B	ASP231
B	HIS342
B	MET390
B	GLY391
B	HIS392
B	MET397
B	PHE401
B	NAD503

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NH4 B 502

Chain	Residue
B	GLN62
B	MET390
B	HIS392
B	HOH635
B	HOH756
D	HOH630

site_id	AC9
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAD B 503

Chain	Residue
B	THR200
B	ASN232
B	GLY261
B	GLY263
B	ASP264
B	VAL265
B	SER283
B	GLU284
B	VAL285
B	ASP286
B	CYS289
B	THR317
B	GLY318
B	ASN319
B	ILE322
B	ILE340
B	GLY341
B	HIS342
B	ASN385
B	HIS392
B	ADN501
B	HOH628
B	HOH631
B	HOH644
B	HOH713
B	HOH735
B	HOH741
A	GLN454
A	LYS467
A	TYR471
B	THR198
B	THR199

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 504

Chain	Residue
A	ARG472
B	VAL426
B	LEU427
B	LYS429
B	ASP432
B	ASP469

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL B 505

Chain	Residue
A	LYS452
A	ASP453
B	PRO33
B	GLU40
B	HOH679
B	HOH697
B	HOH761

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL B 506

Chain	Residue
B	LYS106
B	ARG246
B	GLY387
B	ASN388
B	ALA389
B	HOH645
B	HOH690
B	HOH819

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL B 507

Chain	Residue
B	GLY254
B	ARG279
C	ALA294
C	TYR298
C	GLU299
C	VAL300
D	ILE443
D	GLY444

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT B 508

Chain	Residue
B	LYS106
B	GLN363

site_id	BC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT B 509

Chain	Residue
B	GLY459

site_id	BC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ADN C 501

Chain	Residue
C	HIS58
C	THR60
C	GLN62
C	THR63
C	ASP135
C	GLU197
C	THR198
C	LYS227
C	ASP231
C	HIS342
C	MET390
C	HIS392
C	MET397
C	PHE401
C	NAD503

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NH4 C 502

Chain	Residue
A	HOH663
C	GLN62
C	MET390
C	HIS392
C	HOH676
C	HOH722

site_id	BC9
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAD C 503

Chain	Residue
C	THR198
C	THR199
C	THR200
C	ASN232
C	GLY261
C	GLY263
C	ASP264
C	VAL265
C	SER283
C	GLU284
C	VAL285
C	ASP286
C	CYS289
C	THR317
C	GLY318
C	ASN319
C	ILE322
C	ILE340
C	GLY341
C	HIS342
C	LEU383
C	ASN385
C	HIS392
C	ADN501
C	HOH606
C	HOH613
C	HOH622
C	HOH743
C	HOH750
C	HOH766
D	LYS467
D	TYR471

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 504

Chain	Residue
C	LEU427
C	LYS429
C	ASP432
C	ASP469
D	ARG472

site_id	CC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL C 505

Chain	Residue
A	HOH1026
C	LYS106
C	ARG246
C	GLY387
C	ASN388
C	ALA389
C	HOH739
C	HOH845

site_id	CC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL C 506

Chain	Residue
B	ARG274
B	GLY297
C	ARG274
C	GLY277
C	CYS278
C	ARG279
C	HOH619
C	HOH725
C	HOH765
C	HOH820

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 507

Chain	Residue
C	GLY459
C	PRO465
C	LYS467
C	HOH679
C	HOH883

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT C 508

Chain	Residue
C	ASP344
C	ARG353
C	HOH690

site_id	CC6
Number of Residues	29
Details	BINDING SITE FOR RESIDUE NAD D 501

Chain	Residue
C	LYS467
C	TYR471
D	ASP231
D	ASN232
D	GLY263
D	ASP264
D	VAL265
D	SER283
D	GLU284
D	VAL285
D	ASP286
D	CYS289
D	THR317
D	GLY318
D	ASN319
D	ILE322
D	ILE340
D	GLY341
D	HIS342
D	ASN385
D	HIS392
D	HOH713
D	HOH717
D	HOH718
D	HOH720
D	HOH728
D	HOH780
D	HOH813
D	HOH825

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 502

Chain	Residue
C	HOH926
D	LEU427
D	LYS429
D	ASP432
D	ASP469
D	HOH743
D	HOH811

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 503

Chain	Residue
D	ASN83
D	ILE84
D	TYR113
D	ASP138
D	GLU164

site_id	CC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 504

Chain	Residue
D	LEU233
D	ARG237
D	ALA271
D	HOH732
D	HOH735
D	HOH818
D	HOH847

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 505

Chain	Residue
C	GLU449
C	LEU450
C	GLN462
C	HOH658
D	LYS452
D	ASP456
D	HOH973

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	SER81-ILE95

site_id	PS00739
Number of Residues	18
Details	ADOHCYASE_2 S-adenosyl-L-homocysteine hydrolase signature 2. GKvamVaGFGdVGKGsaA

Chain	Residue	Details
A	GLY254-ALA271

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00563","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	28
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_00563","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_00563","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"26627650","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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