Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2YDX

Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005829	cellular_component	cytosol
A	0006556	biological_process	S-adenosylmethionine biosynthetic process
A	0006730	biological_process	one-carbon metabolic process
A	0019899	molecular_function	enzyme binding
A	0048269	cellular_component	methionine adenosyltransferase complex
A	0048270	molecular_function	methionine adenosyltransferase regulator activity
A	0070062	cellular_component	extracellular exosome
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005829	cellular_component	cytosol
B	0006556	biological_process	S-adenosylmethionine biosynthetic process
B	0006730	biological_process	one-carbon metabolic process
B	0019899	molecular_function	enzyme binding
B	0048269	cellular_component	methionine adenosyltransferase complex
B	0048270	molecular_function	methionine adenosyltransferase regulator activity
B	0070062	cellular_component	extracellular exosome
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005829	cellular_component	cytosol
C	0006556	biological_process	S-adenosylmethionine biosynthetic process
C	0006730	biological_process	one-carbon metabolic process
C	0019899	molecular_function	enzyme binding
C	0048269	cellular_component	methionine adenosyltransferase complex
C	0048270	molecular_function	methionine adenosyltransferase regulator activity
C	0070062	cellular_component	extracellular exosome
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005829	cellular_component	cytosol
D	0006556	biological_process	S-adenosylmethionine biosynthetic process
D	0006730	biological_process	one-carbon metabolic process
D	0019899	molecular_function	enzyme binding
D	0048269	cellular_component	methionine adenosyltransferase complex
D	0048270	molecular_function	methionine adenosyltransferase regulator activity
D	0070062	cellular_component	extracellular exosome
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005829	cellular_component	cytosol
E	0006556	biological_process	S-adenosylmethionine biosynthetic process
E	0006730	biological_process	one-carbon metabolic process
E	0019899	molecular_function	enzyme binding
E	0048269	cellular_component	methionine adenosyltransferase complex
E	0048270	molecular_function	methionine adenosyltransferase regulator activity
E	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE STL A 501

Chain	Residue
A	TRP328
C	ALA77
C	HIS80
C	ASP84
A	ARG329
A	THR331
A	VAL332
A	HIS334
A	GLU336
A	ASN337
C	GLU68
C	ASN76

site_id	AC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE STL A 502

Chain	Residue
A	ARG97
A	SER136
A	ASP137
A	TYR138
A	TYR159
A	ILE184
A	GLU193
A	SER195
A	ALA196
A	ARG219
A	NAP1339

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE STL B 501

Chain	Residue
B	SER136
B	ASP137
B	TYR159
B	ILE184
B	GLU193
B	SER195
B	ALA196
B	ARG219
B	NAP1339
B	SO41342

site_id	AC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE STL B 502

Chain	Residue
B	GLU68
B	ASN76
B	ALA77
B	HIS80
B	ASP84
B	TRP328
B	ARG329
B	THR331
B	VAL332
B	HIS334
B	GLU336
B	ASN337

site_id	AC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE STL C 501

Chain	Residue
A	GLU68
A	ASN76
A	HIS80
A	ASP84
C	TRP328
C	ARG329
C	THR331
C	HIS334
C	GLU336
C	ASN337
C	HOH2095

site_id	AC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE STL C 502

Chain	Residue
C	ARG97
C	SER136
C	ASP137
C	TYR159
C	ILE184
C	GLU193
C	SER195
C	ALA196
C	ARG219
C	NAP1339
C	SO41340

site_id	AC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE STL D 501

Chain	Residue
D	ARG97
D	SER136
D	ASP137
D	TYR159
D	ILE184
D	GLU193
D	SER195
D	ALA196
D	ARG219
D	NAP1339
D	SO41341

site_id	AC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE STL D 502

Chain	Residue
D	TRP328
D	ARG329
D	THR331
D	VAL332
D	HIS334
D	GLU336
D	ASN337
E	GLU68
E	ASP74
E	ASN76
E	ALA77
E	HIS80
E	ASP84

site_id	AC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE STL E 501

Chain	Residue
E	ARG219
E	TXP1339
E	ARG97
E	ARG98
E	SER136
E	ASP137
E	TYR159
E	ILE184
E	GLU193
E	ALA196

site_id	BC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE STL E 502

Chain	Residue
D	GLU68
D	ASP74
D	ASN76
D	ALA77
D	HIS80
D	ASP84
E	TRP328
E	ARG329
E	THR331
E	HIS334
E	GLU336
E	ASN337

site_id	BC2
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAP A 1339

Chain	Residue
A	GLY35
A	THR37
A	GLY38
A	LEU39
A	LEU40
A	PHE60
A	ARG61
A	ARG62
A	VAL70
A	ASN71
A	LEU72
A	CYS93
A	ALA94
A	ALA95
A	ARG97
A	LEU112
A	ILE134
A	SER135
A	TYR159
A	LYS163
A	ILE182
A	PRO183
A	ILE184
A	LEU185
A	STL502
A	HOH2006
A	HOH2025
A	HOH2071
A	HOH2148
A	HOH2149
A	HOH2150
A	HOH2151
A	HOH2152

site_id	BC3
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAP D 1339

Chain	Residue
D	GLY35
D	THR37
D	GLY38
D	LEU39
D	LEU40
D	PHE60
D	ARG61
D	ARG62
D	VAL70
D	ASN71
D	LEU72
D	CYS93
D	ALA94
D	ALA95
D	ARG97
D	LEU112
D	ILE134
D	SER135
D	TYR159
D	LYS163
D	ILE182
D	PRO183
D	LEU185
D	STL501
D	HOH2004
D	HOH2017
D	HOH2063
D	HOH2064

site_id	BC4
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAP C 1339

Chain	Residue
C	GLY35
C	THR37
C	GLY38
C	LEU39
C	LEU40
C	PHE60
C	ARG61
C	ARG62
C	VAL70
C	ASN71
C	LEU72
C	CYS93
C	ALA94
C	ALA95
C	ARG97
C	LEU112
C	ILE134
C	SER135
C	TYR159
C	LYS163
C	ILE182
C	PRO183
C	ILE184
C	LEU185
C	STL502
C	HOH2047
C	HOH2096
C	HOH2097
C	HOH2098
C	HOH2099
C	HOH2100
C	HOH2101

site_id	BC5
Number of Residues	26
Details	BINDING SITE FOR RESIDUE TXP E 1339

Chain	Residue
E	GLY35
E	THR37
E	GLY38
E	LEU39
E	LEU40
E	PHE60
E	ARG61
E	ARG62
E	VAL70
E	ASN71
E	LEU72
E	CYS93
E	ALA94
E	ALA95
E	ARG97
E	LEU112
E	ILE134
E	SER135
E	TYR159
E	LYS163
E	ILE182
E	PRO183
E	LEU185
E	STL501
E	HOH2003
E	HOH2064

site_id	BC6
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAP B 1339

Chain	Residue
B	GLY35
B	THR37
B	GLY38
B	LEU39
B	LEU40
B	PHE60
B	ARG61
B	ARG62
B	VAL70
B	ASN71
B	LEU72
B	CYS93
B	ALA94
B	ALA95
B	ARG97
B	LEU112
B	ILE134
B	SER135
B	TYR159
B	LYS163
B	ILE182
B	PRO183
B	LEU185
B	STL501
B	HOH2004
B	HOH2005
B	HOH2039
B	HOH2067
B	HOH2122
B	HOH2125
B	HOH2126
B	HOH2127

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 E 1340

Chain	Residue
C	ARG30
C	HIS88
E	ARG30
E	HIS88

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 1340

Chain	Residue
A	ARG30
A	HIS88
A	HOH2153
A	HOH2154
D	ARG30
D	HIS88

site_id	BC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 B 1340

Chain	Residue
B	ARG30
B	HIS88

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 1340

Chain	Residue
C	TYR138
C	ARG219
C	ARG289
C	STL502
C	HOH2102
C	HOH2103

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 E 1341

Chain	Residue
E	GLN218
E	GLN255
E	ARG291
E	ASN292

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 1341

Chain	Residue
C	GLN218
C	GLN255
C	ARG291
C	ASN292

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 1341

Chain	Residue
B	GLN218
B	GLN255
B	ARG291
B	ASN292

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 1340

Chain	Residue
D	GLN218
D	GLN255
D	ARG291
D	ASN292

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 1342

Chain	Residue
B	TYR138
B	ALA196
B	ARG219
B	LYS258
B	ARG289
B	STL501

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 1341

Chain	Residue
A	ARG327
A	TRP328
A	ARG329
C	HIS54
C	VAL56

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 1341

Chain	Residue
D	TYR138
D	ALA196
D	ARG219
D	LYS258
D	ARG289
D	STL501

site_id	CC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 1343

Chain	Residue
B	PHE220
B	SER251
B	GLY252
B	ASN253
B	GLN294
B	LEU295
B	ARG308

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 1342

Chain	Residue
A	SER251
A	GLY252
A	ASN253
A	GLN294
A	LEU295
A	ARG308
A	HOH2155

site_id	DC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 1344

Chain	Residue
B	HIS54
B	ARG327
B	TRP328
B	ARG329

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 1342

Chain	Residue
A	HIS54
A	VAL56
C	ARG327
C	TRP328
C	ARG329

site_id	DC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 1342

Chain	Residue
D	ARG327
D	TRP328
D	ARG329
E	HIS54
E	VAL56
E	HOH2017

site_id	DC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 1342

Chain	Residue
D	HIS54
D	VAL56
E	ARG327
E	TRP328
E	ARG329

site_id	DC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 E 1343

Chain	Residue
E	TYR138
E	ARG219
E	LYS258
E	ARG289

site_id	DC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 A 1343

Chain	Residue
A	TYR138
A	HOH2156

site_id	DC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 1344

Chain	Residue
A	ASP137
A	PRO183
A	PHE220
A	HOH2086
A	HOH2098
A	HOH2125

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	35
Details	BINDING: BINDING => ECO:0007744\|PDB:2YDX

Chain	Residue	Details
A	THR37
B	ASN71
B	CYS93
B	ARG97
B	TYR159
B	LEU185
C	THR37
C	PHE60
C	ASN71
C	CYS93
C	ARG97
A	PHE60
C	TYR159
C	LEU185
D	THR37
D	PHE60
D	ASN71
D	CYS93
D	ARG97
D	TYR159
D	LEU185
E	THR37
A	ASN71
E	PHE60
E	ASN71
E	CYS93
E	ARG97
E	TYR159
E	LEU185
A	CYS93
A	ARG97
A	TYR159
A	LEU185
B	THR37
B	PHE60

site_id	SWS_FT_FI2
Number of Residues	5
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	THR309
B	THR309
C	THR309
D	THR309
E	THR309

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