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6QVG

Human SHMT2 in complex with lometrexol

Functional Information from GO Data
ChainGOidnamespacecontents
A0002082biological_processregulation of oxidative phosphorylation
A0003682molecular_functionchromatin binding
A0004372molecular_functionglycine hydroxymethyltransferase activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005743cellular_componentmitochondrial inner membrane
A0005759cellular_componentmitochondrial matrix
A0006417biological_processregulation of translation
A0006544biological_processglycine metabolic process
A0006545biological_processglycine biosynthetic process
A0006563biological_processL-serine metabolic process
A0006564biological_processL-serine biosynthetic process
A0006730biological_processone-carbon metabolic process
A0008284biological_processpositive regulation of cell population proliferation
A0008732molecular_functionL-allo-threonine aldolase activity
A0015943biological_processformate biosynthetic process
A0016597molecular_functionamino acid binding
A0016740molecular_functiontransferase activity
A0019264biological_processglycine biosynthetic process from L-serine
A0030170molecular_functionpyridoxal phosphate binding
A0034340biological_processresponse to type I interferon
A0035999biological_processtetrahydrofolate interconversion
A0042645cellular_componentmitochondrial nucleoid
A0042802molecular_functionidentical protein binding
A0046653biological_processtetrahydrofolate metabolic process
A0051262biological_processprotein tetramerization
A0051289biological_processprotein homotetramerization
A0070013cellular_componentintracellular organelle lumen
A0070062cellular_componentextracellular exosome
A0070129biological_processregulation of mitochondrial translation
A0070536biological_processprotein K63-linked deubiquitination
A0070552cellular_componentBRISC complex
A0120567molecular_functionhydroxytrimethyllysine aldolase activity
A1903715biological_processregulation of aerobic respiration
B0002082biological_processregulation of oxidative phosphorylation
B0003682molecular_functionchromatin binding
B0004372molecular_functionglycine hydroxymethyltransferase activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005743cellular_componentmitochondrial inner membrane
B0005759cellular_componentmitochondrial matrix
B0006417biological_processregulation of translation
B0006544biological_processglycine metabolic process
B0006545biological_processglycine biosynthetic process
B0006563biological_processL-serine metabolic process
B0006564biological_processL-serine biosynthetic process
B0006730biological_processone-carbon metabolic process
B0008284biological_processpositive regulation of cell population proliferation
B0008732molecular_functionL-allo-threonine aldolase activity
B0015943biological_processformate biosynthetic process
B0016597molecular_functionamino acid binding
B0016740molecular_functiontransferase activity
B0019264biological_processglycine biosynthetic process from L-serine
B0030170molecular_functionpyridoxal phosphate binding
B0034340biological_processresponse to type I interferon
B0035999biological_processtetrahydrofolate interconversion
B0042645cellular_componentmitochondrial nucleoid
B0042802molecular_functionidentical protein binding
B0046653biological_processtetrahydrofolate metabolic process
B0051262biological_processprotein tetramerization
B0051289biological_processprotein homotetramerization
B0070013cellular_componentintracellular organelle lumen
B0070062cellular_componentextracellular exosome
B0070129biological_processregulation of mitochondrial translation
B0070536biological_processprotein K63-linked deubiquitination
B0070552cellular_componentBRISC complex
B0120567molecular_functionhydroxytrimethyllysine aldolase activity
B1903715biological_processregulation of aerobic respiration
Functional Information from PDB Data
site_idAC1
Number of Residues10
Detailsbinding site for residue GLY A 601
ChainResidue
APRO140
BHOH747
ATYR141
AARG286
ASER287
AHIS328
AALA331
AHOH720
AHOH780
BHIS328

site_idAC2
Number of Residues7
Detailsbinding site for residue PEG A 602
ChainResidue
AARG66
AARG69
ALEU402
ASER404
AARG486
AHOH771
BGLU110

site_idAC3
Number of Residues3
Detailsbinding site for residue PEG A 603
ChainResidue
AARG494
APHE496
AHOH856

site_idAC4
Number of Residues5
Detailsbinding site for residue NA A 604
ChainResidue
ATRP43
AGLU47
AHOH789
AHOH832
BGLN341

site_idAC5
Number of Residues3
Detailsbinding site for residue GOL A 605
ChainResidue
AALA394
ATHR420
APRO421

site_idAC6
Number of Residues6
Detailsbinding site for residue GOL A 606
ChainResidue
ALEU148
ALEU323
AHOH706
AHOH758
BPRO145
BHOH743

site_idAC7
Number of Residues9
Detailsbinding site for residue DDF A 607
ChainResidue
ALEU166
AGLY170
AHIS171
ALEU172
ALYS181
ASER226
AARG425
BGLU98
BTYR105

site_idAC8
Number of Residues19
Detailsbinding site for residue PLP A 608
ChainResidue
ASER142
AGLY143
ASER144
AHIS171
ATHR225
ASER226
AASP251
AALA253
AHIS254
ATHR277
AHIS279
ALYS280
AHOH853
BTYR96
BGLY325
BGLY326
BHOH740
BHOH760
BHOH835

site_idAC9
Number of Residues2
Detailsbinding site for residue ACT B 601
ChainResidue
BSER417
BTHR420

site_idAD1
Number of Residues11
Detailsbinding site for residue DDF B 602
ChainResidue
AGLU98
ATYR105
AHOH714
BLEU166
BGLY170
BHIS171
BLEU172
BTYR176
BLYS181
BILE183
BARG425

site_idAD2
Number of Residues23
Detailsbinding site for Di-peptide PLP B 603 and LYS B 280
ChainResidue
ATYR96
AGLY325
AGLY326
AHOH729
AHOH740
BSER76
BASN78
BSER142
BGLY143
BSER144
BTHR225
BSER226
BASP251
BALA253
BHIS254
BTHR277
BHIS279
BTHR281
BLEU282
BARG283
BHOH737
BHOH807
BHOH836

Functional Information from PROSITE/UniProt
site_idPS00096
Number of Residues17
DetailsSHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. DIvTTTTHKTLrGARSG
ChainResidueDetails
AASP272-GLY288

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues16
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"29180469","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

249697

PDB entries from 2026-02-25

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