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6PLF

Crystal structure of human PHGDH complexed with Compound 1

Functional Information from GO Data
ChainGOidnamespacecontents
A0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A0051287molecular_functionNAD binding
B0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B0051287molecular_functionNAD binding
Functional Information from PDB Data
site_idAC1
Number of Residues15
Detailsbinding site for residue ONV A 401
ChainResidue
ATYR174
ALEU216
AHOH505
AHOH529
AHOH531
AHOH579
BGLU194
AASP175
APRO176
AILE178
AHIS206
ATHR207
APRO208
ASER212
ATHR213

site_idAC2
Number of Residues7
Detailsbinding site for residue EDO A 402
ChainResidue
AGLU242
APHE262
AASP269
AARG270
ALEU272
AVAL273
AHOH509

site_idAC3
Number of Residues7
Detailsbinding site for residue EDO A 403
ChainResidue
ALYS170
ATHR171
AGLY187
AGLN189
AHOH562
AHOH573
BASP130

site_idAC4
Number of Residues7
Detailsbinding site for residue EDO A 404
ChainResidue
ALEU117
AGLN120
AGLN123
AARG230
AALA255
AHOH502
AHOH533

site_idAC5
Number of Residues16
Detailsbinding site for residue ONV B 401
ChainResidue
AGLU194
AHOH529
BARG155
BTYR174
BASP175
BPRO176
BILE177
BILE178
BLEU193
BHIS206
BTHR207
BPRO208
BSER212
BTHR213
BLEU216
BHOH509

site_idAC6
Number of Residues7
Detailsbinding site for residue EDO B 402
ChainResidue
BGLU242
BPRO267
BASP269
BARG270
BLEU272
BVAL273
BHOH599

site_idAC7
Number of Residues6
Detailsbinding site for residue EDO B 403
ChainResidue
BLEU117
BGLN120
BGLN123
BARG230
BALA255
BASN277

Functional Information from PROSITE/UniProt
site_idPS00065
Number of Residues28
DetailsD_2_HYDROXYACID_DH_1 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. LGILGlGRIGrevatrmqsfgmk.TIgYD
ChainResidueDetails
ALEU148-ASP175

site_idPS00670
Number of Residues23
DetailsD_2_HYDROXYACID_DH_2 D-isomer specific 2-hydroxyacid dehydrogenases signature 2. IWplCDFItVHtPllpsTtgLlN
ChainResidueDetails
AILE196-ASN218

site_idPS00671
Number of Residues17
DetailsD_2_HYDROXYACID_DH_3 D-isomer specific 2-hydroxyacid dehydrogenases signature 3. CKkGvRVVNcARGgIVD
ChainResidueDetails
ACYS225-ASP241

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE:
ChainResidueDetails
AARG236
BARG236

site_idSWS_FT_FI2
Number of Residues2
DetailsACT_SITE: ACT_SITE => ECO:0000250
ChainResidueDetails
AGLU265
BGLU265

site_idSWS_FT_FI3
Number of Residues2
DetailsACT_SITE: Proton donor
ChainResidueDetails
AHIS283
BHIS283

site_idSWS_FT_FI4
Number of Residues14
DetailsBINDING: BINDING => ECO:0000269|Ref.21
ChainResidueDetails
AASP175
ATHR207
ACYS234
AASP260
AHIS283
BTHR78
BARG155
BASP175
BTHR207
BCYS234
BASP260
BHIS283
ATHR78
AARG155

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569
ChainResidueDetails
ASER14
BSER14

site_idSWS_FT_FI6
Number of Residues2
DetailsMOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:Q61753
ChainResidueDetails
ALYS21
BLYS21

site_idSWS_FT_FI7
Number of Residues2
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q61753
ChainResidueDetails
BLYS58
ALYS58

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569
ChainResidueDetails
BTHR78
ATHR78

site_idSWS_FT_FI9
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25114211
ChainResidueDetails
BLYS21
ALYS21

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PDB entries from 2024-06-12

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