Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6SMW

A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with pemetrexed

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004372	molecular_function	glycine hydroxymethyltransferase activity
A	0005739	cellular_component	mitochondrion
A	0006544	biological_process	glycine metabolic process
A	0006563	biological_process	L-serine metabolic process
A	0006730	biological_process	one-carbon metabolic process
A	0008270	molecular_function	zinc ion binding
A	0009536	cellular_component	plastid
A	0016740	molecular_function	transferase activity
A	0019264	biological_process	glycine biosynthetic process from serine
A	0030170	molecular_function	pyridoxal phosphate binding
A	0035999	biological_process	tetrahydrofolate interconversion
A	0045271	cellular_component	respiratory chain complex I
A	0046653	biological_process	tetrahydrofolate metabolic process
A	0050897	molecular_function	cobalt ion binding
B	0004372	molecular_function	glycine hydroxymethyltransferase activity
B	0005739	cellular_component	mitochondrion
B	0006544	biological_process	glycine metabolic process
B	0006563	biological_process	L-serine metabolic process
B	0006730	biological_process	one-carbon metabolic process
B	0008270	molecular_function	zinc ion binding
B	0009536	cellular_component	plastid
B	0016740	molecular_function	transferase activity
B	0019264	biological_process	glycine biosynthetic process from serine
B	0030170	molecular_function	pyridoxal phosphate binding
B	0035999	biological_process	tetrahydrofolate interconversion
B	0045271	cellular_component	respiratory chain complex I
B	0046653	biological_process	tetrahydrofolate metabolic process
B	0050897	molecular_function	cobalt ion binding
C	0004372	molecular_function	glycine hydroxymethyltransferase activity
C	0005739	cellular_component	mitochondrion
C	0006544	biological_process	glycine metabolic process
C	0006563	biological_process	L-serine metabolic process
C	0006730	biological_process	one-carbon metabolic process
C	0008270	molecular_function	zinc ion binding
C	0009536	cellular_component	plastid
C	0016740	molecular_function	transferase activity
C	0019264	biological_process	glycine biosynthetic process from serine
C	0030170	molecular_function	pyridoxal phosphate binding
C	0035999	biological_process	tetrahydrofolate interconversion
C	0045271	cellular_component	respiratory chain complex I
C	0046653	biological_process	tetrahydrofolate metabolic process
C	0050897	molecular_function	cobalt ion binding
D	0004372	molecular_function	glycine hydroxymethyltransferase activity
D	0005739	cellular_component	mitochondrion
D	0006544	biological_process	glycine metabolic process
D	0006563	biological_process	L-serine metabolic process
D	0006730	biological_process	one-carbon metabolic process
D	0008270	molecular_function	zinc ion binding
D	0009536	cellular_component	plastid
D	0016740	molecular_function	transferase activity
D	0019264	biological_process	glycine biosynthetic process from serine
D	0030170	molecular_function	pyridoxal phosphate binding
D	0035999	biological_process	tetrahydrofolate interconversion
D	0045271	cellular_component	respiratory chain complex I
D	0046653	biological_process	tetrahydrofolate metabolic process
D	0050897	molecular_function	cobalt ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	binding site for residue PLS A 701

Chain	Residue
A	SER82
A	HIS260
A	THR283
A	HIS285
A	LYS286
A	ARG430
A	HOH874
B	TYR102
B	GLU104
B	TYR112
B	GLY330
A	SER148
B	GLY331
B	HOH842
A	GLY149
A	SER150
A	HIS177
A	ALA231
A	SER232
A	ASP257
A	ALA259

site_id	AC2
Number of Residues	7
Details	binding site for residue EDO A 702

Chain	Residue
A	GLN126
A	LEU130
A	GLY141
A	VAL142
A	HOH816
A	HOH872
A	HOH933

site_id	AC3
Number of Residues	8
Details	binding site for residue EDO A 703

Chain	Residue
A	PRO151
A	PHE154
A	HOH824
A	HOH829
A	HOH887
A	HOH1115
B	PRO151
B	PHE154

site_id	AC4
Number of Residues	5
Details	binding site for residue EDO A 704

Chain	Residue
A	GLN322
A	ALA323
A	HOH953
B	LYS188
B	ILE189

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO A 705

Chain	Residue
A	GLU61
A	ASP64
A	HOH976
A	HOH1012

site_id	AC6
Number of Residues	6
Details	binding site for residue EDO A 706

Chain	Residue
A	GLU509
A	LYS510
A	GLU511
A	HOH923
D	LYS307
D	GLY309

site_id	AC7
Number of Residues	5
Details	binding site for residue EDO A 707

Chain	Residue
A	ALA159
A	LEU160
A	LEU161
A	ARG319
A	HOH990

site_id	AC8
Number of Residues	5
Details	binding site for residue EDO A 708

Chain	Residue
A	TYR375
A	LYS394
A	ASP454
A	LYS458
A	LEU461

site_id	AC9
Number of Residues	6
Details	binding site for residue EDO A 709

Chain	Residue
A	LYS188
A	ILE189
A	HOH1021
B	GLN322
B	ALA323
B	HOH859

site_id	AD1
Number of Residues	13
Details	binding site for residue LYA A 710

Chain	Residue
A	TYR111
A	HOH801
A	HOH806
A	HOH882
A	HOH914
A	HOH956
A	HOH1118
B	LEU172
B	LEU178
B	THR184
B	LYS187
B	MET424
B	HOH923

site_id	AD2
Number of Residues	4
Details	binding site for residue EDO A 711

Chain	Residue
A	GLY95
A	HOH907
A	HOH1136
B	GLY95

site_id	AD3
Number of Residues	23
Details	binding site for residue PLS B 601

Chain	Residue
B	ALA259
B	HIS260
B	THR283
B	HIS285
B	LYS286
B	ARG430
B	HOH862
B	HOH1005
A	TYR102
A	GLU104
A	TYR112
A	GLY330
A	GLY331
A	HOH910
A	HOH1005
B	SER82
B	SER148
B	GLY149
B	SER150
B	HIS177
B	ALA231
B	SER232
B	ASP257

site_id	AD4
Number of Residues	6
Details	binding site for residue EDO B 602

Chain	Residue
B	ALA159
B	LEU160
B	LEU161
B	LYS162
B	ARG319
B	HOH808

site_id	AD5
Number of Residues	7
Details	binding site for residue EDO B 603

Chain	Residue
B	GLN126
B	LEU130
B	GLY141
B	VAL142
B	HOH756
B	HOH774
B	HOH788

site_id	AD6
Number of Residues	4
Details	binding site for residue EDO B 604

Chain	Residue
B	TYR375
B	LYS394
B	ASP454
B	LYS458

site_id	AD7
Number of Residues	5
Details	binding site for residue EDO B 605

Chain	Residue
A	MET120
B	GLU61
B	ASP64
B	ILE65
B	LEU68

site_id	AD8
Number of Residues	3
Details	binding site for residue EDO B 606

Chain	Residue
A	LYS414
B	ALA109
B	ARG110

site_id	AD9
Number of Residues	3
Details	binding site for residue EDO B 607

Chain	Residue
B	TRP140
B	PHE274
B	HOH1007

site_id	AE1
Number of Residues	6
Details	binding site for residue EDO B 608

Chain	Residue
B	ALA169
B	HIS180
B	GLY181
B	THR198
B	MET199
B	PRO200

site_id	AE2
Number of Residues	5
Details	binding site for residue EDO B 609

Chain	Residue
B	LEU55
B	ALA63
B	GLU67
B	HOH715
B	HOH828

site_id	AE3
Number of Residues	1
Details	binding site for residue EDO B 610

Chain	Residue
A	GLU311

site_id	AE4
Number of Residues	22
Details	binding site for residue PLS C 601

Chain	Residue
C	SER82
C	SER148
C	GLY149
C	SER150
C	HIS177
C	ALA231
C	SER232
C	ASP257
C	ALA259
C	HIS260
C	THR283
C	HIS285
C	LYS286
C	ARG430
C	HOH826
D	TYR102
D	GLU104
D	TYR112
D	GLY330
D	GLY331
D	HOH1427
D	HOH1565

site_id	AE5
Number of Residues	6
Details	binding site for residue EDO C 602

Chain	Residue
C	THR505
C	GLU509
C	LYS510
C	GLU511
C	HOH754
C	HOH758

site_id	AE6
Number of Residues	5
Details	binding site for residue EDO C 603

Chain	Residue
C	TRP140
C	PHE274
C	ARG299
C	HOH769
C	HOH953

site_id	AE7
Number of Residues	3
Details	binding site for residue EDO C 604

Chain	Residue
C	GLU61
C	ASP64
C	HOH797

site_id	AE8
Number of Residues	4
Details	binding site for residue EDO C 605

Chain	Residue
C	LYS471
C	LEU472
C	LYS473
C	HOH778

site_id	AE9
Number of Residues	7
Details	binding site for residue EDO C 606

Chain	Residue
A	GLU368
A	THR369
C	VAL269
C	ASP357
C	HOH786
C	HOH831
C	HOH1010

site_id	AF1
Number of Residues	2
Details	binding site for residue EDO C 607

Chain	Residue
C	ARG236
C	HOH1017

site_id	AF2
Number of Residues	13
Details	binding site for residue LYA C 608

Chain	Residue
C	LEU172
C	LEU178
C	THR184
C	LYS187
C	THR416
C	MET424
C	HOH705
C	HOH721
C	HOH740
C	HOH900
C	HOH932
C	HOH962
D	TYR111

site_id	AF3
Number of Residues	4
Details	binding site for residue EDO C 609

Chain	Residue
C	TYR375
C	ASP454
C	LYS458
C	HOH709

site_id	AF4
Number of Residues	4
Details	binding site for residue EDO C 610

Chain	Residue
C	GLY95
C	HOH796
D	MET91
D	GLY95

site_id	AF5
Number of Residues	5
Details	binding site for residue EDO C 611

Chain	Residue
C	ALA159
C	LEU160
C	LEU161
C	ARG319
C	HOH939

site_id	AF6
Number of Residues	8
Details	binding site for residue EDO C 612

Chain	Residue
C	ALA169
C	LEU170
C	ASP171
C	LEU172
C	GLY181
C	MET199
C	PRO200
C	HOH710

site_id	AF7
Number of Residues	10
Details	binding site for residue SER C 613

Chain	Residue
C	TYR102
C	GLU104
C	TYR112
D	SER82
D	SER232
D	HIS260
D	LYS286
D	ARG430
D	LYA1305
D	PLP1310

site_id	AF8
Number of Residues	9
Details	binding site for residue EDO C 614

Chain	Residue
C	PRO151
C	PHE154
C	LEU328
C	HOH722
C	HOH824
C	HOH1002
D	PRO151
D	PHE154
D	HOH1454

site_id	AF9
Number of Residues	5
Details	binding site for residue EDO C 615

Chain	Residue
C	ILE189
C	HOH935
D	GLN322
D	ALA323
D	HOH1519

site_id	AG1
Number of Residues	6
Details	binding site for residue EDO D 1301

Chain	Residue
C	GLN322
C	PRO326
C	HOH869
D	LYS188
D	ILE189
D	HOH1587

site_id	AG2
Number of Residues	7
Details	binding site for residue EDO D 1302

Chain	Residue
D	GLN126
D	LEU130
D	GLY141
D	VAL142
D	HOH1473
D	HOH1514
D	HOH1598

site_id	AG3
Number of Residues	3
Details	binding site for residue EDO D 1303

Chain	Residue
D	TRP140
D	HOH1409
D	HOH1614

site_id	AG4
Number of Residues	9
Details	binding site for residue EDO D 1304

Chain	Residue
D	ASN206
D	THR207
D	GLY208
D	VAL378
D	SER379
D	GLY380
D	HOH1504
D	HOH1555
D	HOH1596

site_id	AG5
Number of Residues	11
Details	binding site for residue LYA D 1305

Chain	Residue
C	GLU104
C	TYR111
C	SER613
D	LEU178
D	LYS187
D	ILE189
D	MET424
D	HOH1547
D	HOH1587
D	HOH1599
D	HOH1645

site_id	AG6
Number of Residues	6
Details	binding site for residue EDO D 1306

Chain	Residue
D	ALA159
D	LEU160
D	LEU161
D	LYS162
D	ARG319
D	HOH1520

site_id	AG7
Number of Residues	9
Details	binding site for residue EDO D 1307

Chain	Residue
D	ALA169
D	ASP171
D	HIS180
D	GLY181
D	THR198
D	MET199
D	PRO200
D	HOH1483
D	HOH1657

site_id	AG8
Number of Residues	6
Details	binding site for residue EDO D 1308

Chain	Residue
D	TYR276
D	ALA277
D	ARG299
D	TYR314
D	HOH1402
D	HOH1404

site_id	AG9
Number of Residues	6
Details	binding site for residue EDO D 1309

Chain	Residue
C	ASN100
D	ARG72
D	GLU78
D	GLU83
D	ASN84
D	PHE85

site_id	AH1
Number of Residues	25
Details	binding site for Di-peptide PLP D 1310 and LYS D 286

Chain	Residue
C	TYR102
C	GLY330
C	GLY331
C	SER613
C	HOH774
C	HOH864
D	SER82
D	ASN84
D	SER148
D	GLY149
D	SER150
D	HIS177
D	SER179
D	SER232
D	ASP257
D	ALA259
D	HIS260
D	THR283
D	HIS285
D	SER287
D	LEU288
D	ARG289
D	HOH1501
D	HOH1517
D	HOH1718

Functional Information from PROSITE/UniProt

site_id	PS00096
Number of Residues	17
Details	SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. DVvTTTTHKSLrGPRGA

Chain	Residue	Details
A	ASP278-ALA294

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	44
Details	Binding site: {"evidences":[{"source":"PubMed","id":"31873125","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6SMN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6SMW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"31873125","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6SMN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"31873125","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6SMW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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