6PLG
Crystal structure of human PHGDH complexed with Compound 15
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
A | 0051287 | molecular_function | NAD binding |
B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
B | 0051287 | molecular_function | NAD binding |
C | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
C | 0051287 | molecular_function | NAD binding |
D | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
D | 0051287 | molecular_function | NAD binding |
E | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
E | 0051287 | molecular_function | NAD binding |
F | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
F | 0051287 | molecular_function | NAD binding |
G | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
G | 0051287 | molecular_function | NAD binding |
H | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
H | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 14 |
Details | binding site for residue ONS A 401 |
Chain | Residue |
A | GLY154 |
A | THR207 |
A | LEU210 |
A | ARG236 |
C | THR89 |
C | VAL95 |
A | ARG155 |
A | ILE156 |
A | TYR174 |
A | ASP175 |
A | PRO176 |
A | ILE177 |
A | ILE178 |
A | HIS206 |
site_id | AC2 |
Number of Residues | 14 |
Details | binding site for residue ONS B 401 |
Chain | Residue |
B | GLY154 |
B | ARG155 |
B | ILE156 |
B | TYR174 |
B | ASP175 |
B | PRO176 |
B | ILE178 |
B | HIS206 |
B | THR207 |
B | PRO208 |
B | LEU210 |
B | THR213 |
D | THR89 |
D | VAL95 |
site_id | AC3 |
Number of Residues | 13 |
Details | binding site for residue ONS C 401 |
Chain | Residue |
C | GLY152 |
C | ARG155 |
C | ILE156 |
C | TYR174 |
C | ASP175 |
C | PRO176 |
C | ILE178 |
C | HIS206 |
C | THR207 |
C | LEU210 |
C | THR213 |
C | LEU216 |
C | ARG236 |
site_id | AC4 |
Number of Residues | 14 |
Details | binding site for residue ONS D 401 |
Chain | Residue |
D | GLY154 |
D | ARG155 |
D | ILE156 |
D | TYR174 |
D | ASP175 |
D | PRO176 |
D | ILE177 |
D | ILE178 |
D | HIS206 |
D | THR207 |
D | LEU210 |
D | THR213 |
D | LEU216 |
D | ARG236 |
site_id | AC5 |
Number of Residues | 13 |
Details | binding site for residue ONS E 401 |
Chain | Residue |
E | GLY154 |
E | ARG155 |
E | ILE156 |
E | TYR174 |
E | ASP175 |
E | PRO176 |
E | ILE177 |
E | HIS206 |
E | THR207 |
E | SER212 |
E | THR213 |
E | LEU216 |
E | ARG236 |
site_id | AC6 |
Number of Residues | 10 |
Details | binding site for residue MLT E 402 |
Chain | Residue |
A | ARG135 |
E | ARG54 |
E | SER55 |
E | ARG75 |
E | ALA76 |
E | GLY77 |
E | THR78 |
E | HIS283 |
E | ALA286 |
E | GLN292 |
site_id | AC7 |
Number of Residues | 14 |
Details | binding site for residue ONS F 401 |
Chain | Residue |
F | LEU151 |
F | GLY152 |
F | GLY154 |
F | ARG155 |
F | ILE156 |
F | TYR174 |
F | ASP175 |
F | PRO176 |
F | ILE177 |
F | HIS206 |
F | THR207 |
F | PRO208 |
F | LEU216 |
F | ARG236 |
site_id | AC8 |
Number of Residues | 7 |
Details | binding site for residue MLT F 402 |
Chain | Residue |
F | SER55 |
F | ARG75 |
F | ALA76 |
F | GLY77 |
F | THR78 |
F | HIS283 |
F | ALA286 |
site_id | AC9 |
Number of Residues | 13 |
Details | binding site for residue ONS G 401 |
Chain | Residue |
G | GLY154 |
G | ARG155 |
G | ILE156 |
G | TYR174 |
G | ASP175 |
G | PRO176 |
G | ILE177 |
G | HIS206 |
G | THR207 |
G | PRO208 |
G | LEU210 |
G | THR213 |
G | LEU216 |
site_id | AD1 |
Number of Residues | 9 |
Details | binding site for residue MLT G 402 |
Chain | Residue |
C | ARG135 |
G | ARG54 |
G | SER55 |
G | ARG75 |
G | ALA76 |
G | GLY77 |
G | ASN102 |
G | ARG236 |
G | HIS283 |
site_id | AD2 |
Number of Residues | 14 |
Details | binding site for residue ONS H 401 |
Chain | Residue |
H | GLY154 |
H | ARG155 |
H | ILE156 |
H | TYR174 |
H | ASP175 |
H | PRO176 |
H | ILE177 |
H | HIS206 |
H | THR207 |
H | PRO208 |
H | LEU210 |
H | SER212 |
H | THR213 |
H | LEU216 |
site_id | AD3 |
Number of Residues | 11 |
Details | binding site for residue MLT H 402 |
Chain | Residue |
D | ARG135 |
H | ARG54 |
H | SER55 |
H | ARG75 |
H | GLY77 |
H | THR78 |
H | ASN102 |
H | ARG236 |
H | HIS283 |
H | ALA286 |
H | GLN292 |
Functional Information from PROSITE/UniProt
site_id | PS00065 |
Number of Residues | 28 |
Details | D_2_HYDROXYACID_DH_1 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. LGILGlGRIGrevatrmqsfgmk.TIgYD |
Chain | Residue | Details |
A | LEU148-ASP175 |
site_id | PS00670 |
Number of Residues | 23 |
Details | D_2_HYDROXYACID_DH_2 D-isomer specific 2-hydroxyacid dehydrogenases signature 2. IWplCDFItVHtPllpsTtgLlN |
Chain | Residue | Details |
A | ILE196-ASN218 |
site_id | PS00671 |
Number of Residues | 17 |
Details | D_2_HYDROXYACID_DH_3 D-isomer specific 2-hydroxyacid dehydrogenases signature 3. CKkGvRVVNcARGgIVD |
Chain | Residue | Details |
A | CYS225-ASP241 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 8 |
Details | ACT_SITE: |
Chain | Residue | Details |
A | ARG236 | |
B | ARG236 | |
C | ARG236 | |
D | ARG236 | |
E | ARG236 | |
F | ARG236 | |
G | ARG236 | |
H | ARG236 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | ACT_SITE: ACT_SITE => ECO:0000250 |
Chain | Residue | Details |
C | GLU265 | |
D | GLU265 | |
E | GLU265 | |
F | GLU265 | |
G | GLU265 | |
H | GLU265 | |
A | GLU265 | |
B | GLU265 |
site_id | SWS_FT_FI3 |
Number of Residues | 8 |
Details | ACT_SITE: Proton donor |
Chain | Residue | Details |
B | HIS283 | |
C | HIS283 | |
F | HIS283 | |
G | HIS283 | |
H | HIS283 | |
A | HIS283 | |
D | HIS283 | |
E | HIS283 |
site_id | SWS_FT_FI4 |
Number of Residues | 56 |
Details | BINDING: BINDING => ECO:0000269|Ref.21 |
Chain | Residue | Details |
B | ARG155 | |
B | ASP175 | |
B | THR207 | |
B | CYS234 | |
B | ASP260 | |
B | HIS283 | |
C | THR78 | |
C | ARG155 | |
C | ASP175 | |
C | THR207 | |
C | CYS234 | |
C | ASP260 | |
C | HIS283 | |
D | THR78 | |
D | ARG155 | |
D | ASP175 | |
D | THR207 | |
D | CYS234 | |
D | ASP260 | |
D | HIS283 | |
E | THR78 | |
E | ARG155 | |
E | ASP175 | |
E | THR207 | |
E | CYS234 | |
E | ASP260 | |
E | HIS283 | |
F | THR78 | |
F | ARG155 | |
F | ASP175 | |
F | THR207 | |
F | CYS234 | |
F | ASP260 | |
F | HIS283 | |
G | THR78 | |
G | ARG155 | |
G | ASP175 | |
G | THR207 | |
G | CYS234 | |
G | ASP260 | |
G | HIS283 | |
H | THR78 | |
H | ARG155 | |
H | ASP175 | |
H | THR207 | |
H | CYS234 | |
H | ASP260 | |
H | HIS283 | |
A | ARG155 | |
A | ASP175 | |
A | THR207 | |
A | CYS234 | |
A | ASP260 | |
A | HIS283 | |
B | THR78 | |
A | THR78 |
site_id | SWS_FT_FI5 |
Number of Residues | 8 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
A | SER14 | |
B | SER14 | |
C | SER14 | |
D | SER14 | |
E | SER14 | |
F | SER14 | |
G | SER14 | |
H | SER14 |
site_id | SWS_FT_FI6 |
Number of Residues | 8 |
Details | MOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:Q61753 |
Chain | Residue | Details |
B | LYS21 | |
F | LYS21 | |
G | LYS21 | |
H | LYS21 | |
A | LYS21 | |
C | LYS21 | |
D | LYS21 | |
E | LYS21 |
site_id | SWS_FT_FI7 |
Number of Residues | 8 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q61753 |
Chain | Residue | Details |
B | LYS58 | |
F | LYS58 | |
G | LYS58 | |
H | LYS58 | |
A | LYS58 | |
C | LYS58 | |
D | LYS58 | |
E | LYS58 |
site_id | SWS_FT_FI8 |
Number of Residues | 8 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
B | THR78 | |
F | THR78 | |
G | THR78 | |
H | THR78 | |
A | THR78 | |
C | THR78 | |
D | THR78 | |
E | THR78 |
site_id | SWS_FT_FI9 |
Number of Residues | 16 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25114211 |
Chain | Residue | Details |
E | LYS21 | |
F | LYS21 | |
G | LYS21 | |
H | LYS21 | |
D | LYS21 | |
A | LYS21 | |
B | LYS21 | |
C | LYS21 |