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4PCU

Crystal structure of delta516-525 E201S human cystathionine beta-synthase with AdoMet

Functional Information from GO Data
ChainGOidnamespacecontents
A0001958biological_processendochondral ossification
A0001974biological_processblood vessel remodeling
A0004122molecular_functioncystathionine beta-synthase activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006534biological_processcysteine metabolic process
A0006535biological_processcysteine biosynthetic process from serine
A0006563biological_processL-serine metabolic process
A0006565biological_processL-serine catabolic process
A0006801biological_processsuperoxide metabolic process
A0009069biological_processserine family amino acid metabolic process
A0010749biological_processregulation of nitric oxide mediated signal transduction
A0016829molecular_functionlyase activity
A0019343biological_processcysteine biosynthetic process via cystathionine
A0019344biological_processcysteine biosynthetic process
A0019346biological_processtranssulfuration
A0019448biological_processL-cysteine catabolic process
A0019825molecular_functionoxygen binding
A0019899molecular_functionenzyme binding
A0020037molecular_functionheme binding
A0021587biological_processcerebellum morphogenesis
A0030170molecular_functionpyridoxal phosphate binding
A0031625molecular_functionubiquitin protein ligase binding
A0031667biological_processresponse to nutrient levels
A0042262biological_processDNA protection
A0042802molecular_functionidentical protein binding
A0042803molecular_functionprotein homodimerization activity
A0043066biological_processnegative regulation of apoptotic process
A0043418biological_processhomocysteine catabolic process
A0044272biological_processsulfur compound biosynthetic process
A0046872molecular_functionmetal ion binding
A0050421molecular_functionnitrite reductase (NO-forming) activity
A0050667biological_processhomocysteine metabolic process
A0051593biological_processresponse to folic acid
A0060135biological_processmaternal process involved in female pregnancy
A0060351biological_processcartilage development involved in endochondral bone morphogenesis
A0070025molecular_functioncarbon monoxide binding
A0070026molecular_functionnitric oxide binding
A0070814biological_processhydrogen sulfide biosynthetic process
A0071456biological_processcellular response to hypoxia
A0072341molecular_functionmodified amino acid binding
A0097746biological_processblood vessel diameter maintenance
A1904047molecular_functionS-adenosyl-L-methionine binding
B0001958biological_processendochondral ossification
B0001974biological_processblood vessel remodeling
B0004122molecular_functioncystathionine beta-synthase activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006534biological_processcysteine metabolic process
B0006535biological_processcysteine biosynthetic process from serine
B0006563biological_processL-serine metabolic process
B0006565biological_processL-serine catabolic process
B0006801biological_processsuperoxide metabolic process
B0009069biological_processserine family amino acid metabolic process
B0010749biological_processregulation of nitric oxide mediated signal transduction
B0016829molecular_functionlyase activity
B0019343biological_processcysteine biosynthetic process via cystathionine
B0019344biological_processcysteine biosynthetic process
B0019346biological_processtranssulfuration
B0019448biological_processL-cysteine catabolic process
B0019825molecular_functionoxygen binding
B0019899molecular_functionenzyme binding
B0020037molecular_functionheme binding
B0021587biological_processcerebellum morphogenesis
B0030170molecular_functionpyridoxal phosphate binding
B0031625molecular_functionubiquitin protein ligase binding
B0031667biological_processresponse to nutrient levels
B0042262biological_processDNA protection
B0042802molecular_functionidentical protein binding
B0042803molecular_functionprotein homodimerization activity
B0043066biological_processnegative regulation of apoptotic process
B0043418biological_processhomocysteine catabolic process
B0044272biological_processsulfur compound biosynthetic process
B0046872molecular_functionmetal ion binding
B0050421molecular_functionnitrite reductase (NO-forming) activity
B0050667biological_processhomocysteine metabolic process
B0051593biological_processresponse to folic acid
B0060135biological_processmaternal process involved in female pregnancy
B0060351biological_processcartilage development involved in endochondral bone morphogenesis
B0070025molecular_functioncarbon monoxide binding
B0070026molecular_functionnitric oxide binding
B0070814biological_processhydrogen sulfide biosynthetic process
B0071456biological_processcellular response to hypoxia
B0072341molecular_functionmodified amino acid binding
B0097746biological_processblood vessel diameter maintenance
B1904047molecular_functionS-adenosyl-L-methionine binding
Functional Information from PDB Data
site_idAC1
Number of Residues19
Detailsbinding site for residue HEM A 601
ChainResidue
APRO49
APRO64
AHIS65
AALA226
APRO229
ATYR233
AGLY263
AARG266
ATHR313
BARG58
BHEM601
ASER50
AARG51
ACYS52
ATHR53
ATRP54
APRO59
AGLU62
ASER63

site_idAC2
Number of Residues13
Detailsbinding site for residue PLP A 602
ChainResidue
ALYS119
AASN149
ASER254
AGLY256
ATHR257
AGLY258
ATHR260
AGLU304
AGLY305
AILE306
ASER349
APRO375
AASP376

site_idAC3
Number of Residues12
Detailsbinding site for residue SAM A 603
ChainResidue
AALA421
APRO422
ALEU423
AGLY442
APHE443
AASP444
AGLN445
AVAL533
ATHR535
AILE537
AASP538
BSAM603

site_idAC4
Number of Residues20
Detailsbinding site for residue HEM B 601
ChainResidue
AARG58
AHEM601
BPRO49
BSER50
BARG51
BCYS52
BTHR53
BTRP54
BPRO59
BGLU62
BSER63
BPRO64
BHIS65
BARG224
BALA226
BPRO229
BTYR233
BGLY263
BARG266
BTHR313

site_idAC5
Number of Residues13
Detailsbinding site for residue PLP B 602
ChainResidue
BLYS119
BASN149
BSER254
BGLY256
BTHR257
BGLY258
BTHR260
BGLU304
BGLY305
BILE306
BSER349
BPRO375
BASP376

site_idAC6
Number of Residues12
Detailsbinding site for residue SAM B 603
ChainResidue
AGLY442
AASP444
ASAM603
BLEU423
BGLY442
BPHE443
BASP444
BGLN445
BVAL533
BTHR535
BILE537
BASP538

Functional Information from PROSITE/UniProt
site_idPS00901
Number of Residues19
DetailsCYS_SYNTHASE Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. KcEffn.AGgSVKdRiSlrM
ChainResidueDetails
ALYS108-MET126

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsBINDING: axial binding residue => ECO:0000269|PubMed:11483494, ECO:0000269|PubMed:12173932
ChainResidueDetails
ACYS52
AHIS65
BCYS52
BHIS65

site_idSWS_FT_FI2
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:11483494, ECO:0000269|PubMed:12173932
ChainResidueDetails
AASN149
AGLY256
ASER349
BASN149
BGLY256
BSER349

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692
ChainResidueDetails
ASER27
BSER27

site_idSWS_FT_FI4
Number of Residues2
DetailsMOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:11483494, ECO:0000269|PubMed:12173932
ChainResidueDetails
ALYS119
BLYS119

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163
ChainResidueDetails
ASER199
BSER199

site_idSWS_FT_FI6
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) => ECO:0000269|PubMed:17087506
ChainResidueDetails
ALYS211
BLYS211

Catalytic Information from CSA
site_idMCSA1
Number of Residues1
DetailsM-CSA 713
ChainResidueDetails
ALYS119covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay

site_idMCSA2
Number of Residues1
DetailsM-CSA 713
ChainResidueDetails
BLYS119covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay

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PDB entries from 2024-07-31

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