Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6VD0

Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with free Methionine and AMPCPP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004478	molecular_function	methionine adenosyltransferase activity
A	0005507	molecular_function	copper ion binding
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005730	cellular_component	nucleolus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006556	biological_process	S-adenosylmethionine biosynthetic process
A	0006730	biological_process	one-carbon metabolic process
A	0009505	cellular_component	plant-type cell wall
A	0009506	cellular_component	plasmodesma
A	0016740	molecular_function	transferase activity
A	0046872	molecular_function	metal ion binding
A	0070062	cellular_component	extracellular exosome
B	0004478	molecular_function	methionine adenosyltransferase activity
B	0005507	molecular_function	copper ion binding
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006556	biological_process	S-adenosylmethionine biosynthetic process
B	0006730	biological_process	one-carbon metabolic process
B	0009505	cellular_component	plant-type cell wall
B	0009506	cellular_component	plasmodesma
B	0016740	molecular_function	transferase activity
B	0046872	molecular_function	metal ion binding
B	0070062	cellular_component	extracellular exosome
C	0004478	molecular_function	methionine adenosyltransferase activity
C	0005507	molecular_function	copper ion binding
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005730	cellular_component	nucleolus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006556	biological_process	S-adenosylmethionine biosynthetic process
C	0006730	biological_process	one-carbon metabolic process
C	0009505	cellular_component	plant-type cell wall
C	0009506	cellular_component	plasmodesma
C	0016740	molecular_function	transferase activity
C	0046872	molecular_function	metal ion binding
C	0070062	cellular_component	extracellular exosome
D	0004478	molecular_function	methionine adenosyltransferase activity
D	0005507	molecular_function	copper ion binding
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005730	cellular_component	nucleolus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006556	biological_process	S-adenosylmethionine biosynthetic process
D	0006730	biological_process	one-carbon metabolic process
D	0009505	cellular_component	plant-type cell wall
D	0009506	cellular_component	plasmodesma
D	0016740	molecular_function	transferase activity
D	0046872	molecular_function	metal ion binding
D	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	31
Details	binding site for residue APC A 401

Chain	Residue
A	HIS15
A	ARG252
A	LYS253
A	MG404
A	K406
A	HOH513
A	HOH523
A	HOH544
A	HOH589
A	HOH613
B	ASP102
A	PRO16
B	ILE103
B	ASP122
B	GLY268
B	ALA269
B	LYS273
B	ASP279
B	ILE310
B	MET402
B	MG404
B	HOH539
A	ASP17
B	HOH550
B	HOH592
A	ASP167
A	LYS169
A	SER235
A	ARG237
A	PHE238
A	ASP246

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

Chain	Residue
A	ALA41
A	GLU56
A	GLN99
A	ILE103
A	LYS277
A	HOH562
A	HOH578
B	ASP246
B	APC401
B	HOH512
B	HOH525

site_id	AC3
Number of Residues	5
Details	binding site for residue MG A 403

Chain	Residue
A	HOH517
A	HOH598
B	APC401
B	HOH544
B	HOH552

site_id	AC4
Number of Residues	5
Details	binding site for residue MG A 404

Chain	Residue
A	ASP17
A	LYS253
A	APC401
A	HOH613
A	HOH637

site_id	AC5
Number of Residues	6
Details	binding site for residue MG A 405

Chain	Residue
A	HOH529
A	HOH644
A	HOH759
D	HOH517
D	HOH523
D	HOH713

site_id	AC6
Number of Residues	6
Details	binding site for residue K A 406

Chain	Residue
A	ASP246
A	ALA247
A	APC401
A	HOH613
B	GLU43
B	HOH604

site_id	AC7
Number of Residues	3
Details	binding site for residue PEG A 407

Chain	Residue
A	MET183
A	HOH550
B	PHE319

site_id	AC8
Number of Residues	9
Details	binding site for residue MPO A 408

Chain	Residue
A	ASP37
A	LYS39
A	HIS108
A	PHE111
A	THR112
A	LYS113
A	ARG114
A	ILE118
A	LYS355

site_id	AC9
Number of Residues	33
Details	binding site for residue APC B 401

Chain	Residue
B	ARG252
B	LYS253
B	MG403
B	K405
B	HOH512
B	HOH544
B	HOH546
B	HOH569
B	HOH571
B	HOH574
A	ASP102
A	ILE103
A	ASP122
A	GLY268
A	ALA269
A	LYS273
A	ASP279
A	ILE310
A	MET402
A	MG403
A	HOH517
A	HOH525
A	HOH581
A	HOH598
B	HIS15
B	PRO16
B	ASP17
B	ASP167
B	LYS169
B	SER235
B	ARG237
B	PHE238
B	ASP246

site_id	AD1
Number of Residues	12
Details	binding site for residue MET B 402

Chain	Residue
A	ASP246
A	APC401
A	HOH513
A	HOH532
B	ALA41
B	GLU56
B	GLN99
B	ILE103
B	GLY121
B	LYS277
B	HOH558
B	HOH661

site_id	AD2
Number of Residues	6
Details	binding site for residue MG B 403

Chain	Residue
B	ASP17
B	LYS253
B	APC401
B	K405
B	HOH571
B	HOH574

site_id	AD3
Number of Residues	5
Details	binding site for residue MG B 404

Chain	Residue
A	APC401
A	HOH544
A	HOH589
B	HOH539
B	HOH603

site_id	AD4
Number of Residues	7
Details	binding site for residue K B 405

Chain	Residue
A	GLU43
A	HOH683
B	ASP246
B	ALA247
B	APC401
B	MG403
B	HOH574

site_id	AD5
Number of Residues	3
Details	binding site for residue PEG B 406

Chain	Residue
A	PHE319
B	GLY261
B	HOH653

site_id	AD6
Number of Residues	8
Details	binding site for residue MPO B 407

Chain	Residue
B	ASP37
B	LYS39
B	HIS108
B	PHE111
B	THR112
B	ARG114
B	LYS355
B	HOH683

site_id	AD7
Number of Residues	3
Details	binding site for residue PG4 C 401

Chain	Residue
C	ASN178
C	HOH582
C	HOH638

site_id	AD8
Number of Residues	32
Details	binding site for residue APC C 402

Chain	Residue
C	HIS15
C	PRO16
C	ASP17
C	ASP167
C	LYS169
C	SER235
C	ARG237
C	PHE238
C	ASP246
C	ARG252
C	LYS253
C	MG405
C	MG406
C	K407
C	HOH504
C	HOH555
C	HOH579
C	HOH610
C	HOH653
D	ASP102
D	ILE103
D	ASP122
D	GLY268
D	ALA269
D	LYS273
D	ASP279
D	ILE310
D	MET402
D	HOH536
D	HOH537
D	HOH565
D	HOH594

site_id	AD9
Number of Residues	12
Details	binding site for residue MET C 403

Chain	Residue
C	ALA41
C	GLU56
C	GLN99
C	ILE103
C	GLY121
C	LYS277
C	ILE310
C	HOH510
C	HOH640
D	ASP246
D	APC401
D	HOH566

site_id	AE1
Number of Residues	5
Details	binding site for residue MG C 404

Chain	Residue
C	HOH515
C	HOH586
C	HOH625
D	APC401
D	HOH590

site_id	AE2
Number of Residues	5
Details	binding site for residue MG C 405

Chain	Residue
C	ASP17
C	LYS253
C	APC402
C	HOH504
C	HOH653

site_id	AE3
Number of Residues	5
Details	binding site for residue MG C 406

Chain	Residue
C	APC402
C	HOH541
C	HOH610
D	HOH536
D	HOH594

site_id	AE4
Number of Residues	6
Details	binding site for residue K C 407

Chain	Residue
C	ASP246
C	ALA247
C	APC402
C	HOH579
D	GLU43
D	HOH648

site_id	AE5
Number of Residues	7
Details	binding site for residue MPO C 408

Chain	Residue
C	ASP37
C	LYS39
C	HIS108
C	PHE111
C	LYS113
C	ILE118
C	LYS355

site_id	AE6
Number of Residues	30
Details	binding site for residue APC D 401

Chain	Residue
C	ASP102
C	ILE103
C	ASP122
C	ALA269
C	LYS273
C	ASP279
C	ILE310
C	MET403
C	MG404
C	HOH515
D	HIS15
D	PRO16
D	ASP17
D	ASP167
D	LYS169
D	SER235
D	ARG237
D	PHE238
D	ASP246
D	ARG252
D	LYS253
D	MG403
D	K404
D	HOH550
D	HOH566
D	HOH577
D	HOH590
D	HOH601
D	HOH617
D	HOH657

site_id	AE7
Number of Residues	12
Details	binding site for residue MET D 402

Chain	Residue
C	ASP246
C	APC402
C	HOH579
D	ALA41
D	GLU56
D	GLN99
D	ILE103
D	GLY121
D	LYS277
D	HOH520
D	HOH588
D	HOH632

site_id	AE8
Number of Residues	5
Details	binding site for residue MG D 403

Chain	Residue
D	ASP17
D	LYS253
D	APC401
D	HOH601
D	HOH617

site_id	AE9
Number of Residues	6
Details	binding site for residue K D 404

Chain	Residue
C	GLU43
C	HOH645
D	ASP246
D	ALA247
D	APC401
D	HOH601

site_id	AF1
Number of Residues	13
Details	binding site for residue MPO D 405

Chain	Residue
D	ASP37
D	LYS39
D	HIS108
D	PHE111
D	THR112
D	LYS113
D	ARG114
D	PRO115
D	ILE118
D	LYS355
D	HOH548
D	HOH611
D	HOH663

Functional Information from PROSITE/UniProt

site_id	PS00376
Number of Residues	11
Details	ADOMET_SYNTHASE_1 S-adenosylmethionine synthase signature 1. GAGDQGhmfGY

Chain	Residue	Details
A	GLY119-TYR129

site_id	PS00377
Number of Residues	9
Details	ADOMET_SYNTHASE_2 S-adenosylmethionine synthase signature 2. GGGAFSgKD

Chain	Residue	Details
A	GLY266-ASP274

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P13444

Chain	Residue	Details
A	GLU9
B	GLU9
C	GLU9
D	GLU9

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: in other chain => ECO:0000250\|UniProtKB:Q00266

Chain	Residue	Details
A	HIS15
D	HIS15
D	ASP167
D	SER235
A	ASP167
A	SER235
B	HIS15
B	ASP167
B	SER235
C	HIS15
C	ASP167
C	SER235

site_id	SWS_FT_FI3
Number of Residues	16
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P0A817

Chain	Residue	Details
A	GLU43
C	ASP246
C	ALA269
C	LYS273
D	GLU43
D	ASP246
D	ALA269
D	LYS273
A	ASP246
A	ALA269
A	LYS273
B	GLU43
B	ASP246
B	ALA269
B	LYS273
C	GLU43

site_id	SWS_FT_FI4
Number of Residues	16
Details	BINDING: in other chain => ECO:0000250\|UniProtKB:P0A817

Chain	Residue	Details
A	GLU56
C	GLN99
C	ARG252
C	LYS277
D	GLU56
D	GLN99
D	ARG252
D	LYS277
A	GLN99
A	ARG252
A	LYS277
B	GLU56
B	GLN99
B	ARG252
B	LYS277
C	GLU56

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