4BZC
Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE T8T A 700 |
| Chain | Residue |
| A | GLN149 |
| A | TYR315 |
| A | ASP319 |
| A | ARG366 |
| A | HIS370 |
| A | TYR374 |
| A | GLN375 |
| A | MN750 |
| A | HOH2007 |
| A | HOH2011 |
| A | LEU150 |
| A | ARG164 |
| A | ASP207 |
| A | HIS210 |
| A | HIS215 |
| A | HIS233 |
| A | ASP311 |
| A | LYS312 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN A 750 |
| Chain | Residue |
| A | HIS167 |
| A | HIS206 |
| A | ASP207 |
| A | ASP311 |
| A | T8T700 |
| site_id | AC3 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE T8T A 800 |
| Chain | Residue |
| A | VAL156 |
| A | PHE157 |
| A | GLY324 |
| A | ARG372 |
| A | HIS376 |
| A | LYS377 |
| A | T8T900 |
| A | MG950 |
| A | HOH2012 |
| A | HOH2013 |
| C | ARG333 |
| C | PHE337 |
| C | ARG352 |
| C | LYS354 |
| C | ASN358 |
| C | LYS523 |
| D | VAL117 |
| D | ASN119 |
| D | HIS125 |
| site_id | AC4 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE T8T A 900 |
| Chain | Residue |
| A | TYR155 |
| A | VAL156 |
| A | LYS377 |
| A | VAL378 |
| A | ARG451 |
| A | T8T800 |
| A | MG950 |
| A | HOH2012 |
| A | HOH2014 |
| C | LYS523 |
| D | LYS116 |
| D | VAL117 |
| D | ILE118 |
| D | ASP137 |
| D | GLN142 |
| D | ARG145 |
| D | PHE165 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 950 |
| Chain | Residue |
| A | T8T800 |
| A | T8T900 |
| A | HOH2012 |
| D | LYS116 |
| site_id | AC6 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE T8T B 700 |
| Chain | Residue |
| B | GLN149 |
| B | LEU150 |
| B | ARG164 |
| B | ASP207 |
| B | HIS210 |
| B | HIS215 |
| B | HIS233 |
| B | ASP311 |
| B | LYS312 |
| B | TYR315 |
| B | ASP319 |
| B | ARG366 |
| B | HIS370 |
| B | TYR374 |
| B | GLN375 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN B 750 |
| Chain | Residue |
| B | HIS167 |
| B | HIS206 |
| B | ASP207 |
| B | ASP311 |
| site_id | AC8 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE T8T B 800 |
| Chain | Residue |
| D | LYS523 |
| B | VAL156 |
| B | PHE157 |
| B | GLY324 |
| B | ILE325 |
| B | ARG372 |
| B | HIS376 |
| B | LYS377 |
| B | T8T900 |
| B | MG950 |
| B | HOH2009 |
| C | VAL117 |
| C | ASN119 |
| D | ARG333 |
| D | PHE337 |
| D | ARG352 |
| D | LYS354 |
| D | ASN358 |
| site_id | AC9 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE T8T B 900 |
| Chain | Residue |
| B | TYR155 |
| B | VAL156 |
| B | VAL378 |
| B | ARG451 |
| B | LYS455 |
| B | T8T800 |
| B | MG950 |
| B | HOH2007 |
| C | LYS116 |
| C | VAL117 |
| C | ILE118 |
| C | ASP137 |
| C | GLN142 |
| C | ARG145 |
| C | PHE165 |
| D | LYS523 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG B 950 |
| Chain | Residue |
| B | T8T800 |
| B | T8T900 |
| C | LYS116 |
| site_id | BC2 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE T8T C 700 |
| Chain | Residue |
| C | GLN149 |
| C | LEU150 |
| C | ARG164 |
| C | ASP207 |
| C | HIS210 |
| C | HIS215 |
| C | HIS233 |
| C | ASP311 |
| C | LYS312 |
| C | TYR315 |
| C | ASP319 |
| C | ARG366 |
| C | TYR374 |
| C | GLN375 |
| C | MN750 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN C 750 |
| Chain | Residue |
| C | HIS167 |
| C | HIS206 |
| C | ASP207 |
| C | ASP311 |
| C | T8T700 |
| site_id | BC4 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE T8T C 800 |
| Chain | Residue |
| A | ASP330 |
| A | ARG333 |
| A | PHE337 |
| A | ARG352 |
| A | LYS354 |
| A | ASN358 |
| A | LYS523 |
| B | VAL117 |
| B | ASN119 |
| C | VAL156 |
| C | PHE157 |
| C | GLY324 |
| C | ILE325 |
| C | ARG372 |
| C | HIS376 |
| C | LYS377 |
| C | T8T900 |
| C | MG950 |
| site_id | BC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE T8T C 900 |
| Chain | Residue |
| A | LYS523 |
| B | LYS116 |
| B | VAL117 |
| B | ILE118 |
| B | ASP137 |
| B | GLN142 |
| B | ARG145 |
| B | PHE165 |
| C | TYR155 |
| C | VAL156 |
| C | VAL378 |
| C | ARG451 |
| C | LYS455 |
| C | T8T800 |
| C | MG950 |
| site_id | BC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG C 950 |
| Chain | Residue |
| A | LYS523 |
| B | LYS116 |
| C | T8T800 |
| C | T8T900 |
| site_id | BC7 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE T8T D 700 |
| Chain | Residue |
| D | GLN149 |
| D | LEU150 |
| D | ARG164 |
| D | ASP207 |
| D | HIS210 |
| D | HIS215 |
| D | HIS233 |
| D | ASP311 |
| D | LYS312 |
| D | TYR315 |
| D | ASP319 |
| D | TYR374 |
| D | GLN375 |
| D | MN750 |
| site_id | BC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN D 750 |
| Chain | Residue |
| D | HIS167 |
| D | HIS206 |
| D | ASP207 |
| D | ASP311 |
| D | T8T700 |
| site_id | BC9 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE T8T D 800 |
| Chain | Residue |
| A | VAL117 |
| A | ASN119 |
| B | ASP330 |
| B | ARG333 |
| B | PHE337 |
| B | ARG352 |
| B | LYS354 |
| B | LYS523 |
| D | VAL156 |
| D | PHE157 |
| D | GLY324 |
| D | ILE325 |
| D | ARG372 |
| D | HIS376 |
| D | LYS377 |
| D | T8T900 |
| D | MG950 |
| site_id | CC1 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE T8T D 900 |
| Chain | Residue |
| A | LYS116 |
| A | VAL117 |
| A | ILE118 |
| A | ASP137 |
| A | GLN142 |
| A | ARG145 |
| A | PHE165 |
| B | LYS523 |
| D | TYR155 |
| D | VAL156 |
| D | LYS377 |
| D | VAL378 |
| D | ARG451 |
| D | T8T800 |
| D | MG950 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG D 950 |
| Chain | Residue |
| A | LYS116 |
| D | T8T800 |
| D | T8T900 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: ACT_SITE => ECO:0000305|PubMed:22056990 |
| Chain | Residue | Details |
| A | HIS233 | |
| B | HIS233 | |
| C | HIS233 | |
| D | HIS233 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 20 |
| Details | BINDING: in chain B => ECO:0000269|PubMed:25267621, ECO:0007744|PDB:4TNP, ECO:0007744|PDB:4TNQ, ECO:0007744|PDB:4TNR, ECO:0007744|PDB:4TNX |
| Chain | Residue | Details |
| A | LYS116 | |
| B | ARG145 | |
| C | LYS116 | |
| C | VAL117 | |
| C | ASP137 | |
| C | GLN142 | |
| C | ARG145 | |
| D | LYS116 | |
| D | VAL117 | |
| D | ASP137 | |
| D | GLN142 | |
| A | VAL117 | |
| D | ARG145 | |
| A | ASP137 | |
| A | GLN142 | |
| A | ARG145 | |
| B | LYS116 | |
| B | VAL117 | |
| B | ASP137 | |
| B | GLN142 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: in chain B => ECO:0000269|PubMed:25267621, ECO:0007744|PDB:4TNQ |
| Chain | Residue | Details |
| A | ASN119 | |
| B | ASN119 | |
| C | ASN119 | |
| D | ASN119 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 32 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:25267621, ECO:0007744|PDB:4TNQ |
| Chain | Residue | Details |
| A | GLN149 | |
| B | ARG164 | |
| B | HIS210 | |
| B | HIS215 | |
| B | LYS312 | |
| B | TYR315 | |
| B | ASP319 | |
| B | GLN375 | |
| C | GLN149 | |
| C | ARG164 | |
| C | HIS210 | |
| A | ARG164 | |
| C | HIS215 | |
| C | LYS312 | |
| C | TYR315 | |
| C | ASP319 | |
| C | GLN375 | |
| D | GLN149 | |
| D | ARG164 | |
| D | HIS210 | |
| D | HIS215 | |
| D | LYS312 | |
| A | HIS210 | |
| D | TYR315 | |
| D | ASP319 | |
| D | GLN375 | |
| A | HIS215 | |
| A | LYS312 | |
| A | TYR315 | |
| A | ASP319 | |
| A | GLN375 | |
| B | GLN149 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 28 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:24141705, ECO:0007744|PDB:4BZB |
| Chain | Residue | Details |
| A | LEU150 | |
| B | HIS206 | |
| B | ASP207 | |
| B | ASP311 | |
| B | ARG366 | |
| B | TYR374 | |
| C | LEU150 | |
| C | HIS167 | |
| C | HIS206 | |
| C | ASP207 | |
| C | ASP311 | |
| A | HIS167 | |
| C | ARG366 | |
| C | TYR374 | |
| D | LEU150 | |
| D | HIS167 | |
| D | HIS206 | |
| D | ASP207 | |
| D | ASP311 | |
| D | ARG366 | |
| D | TYR374 | |
| A | HIS206 | |
| A | ASP207 | |
| A | ASP311 | |
| A | ARG366 | |
| A | TYR374 | |
| B | LEU150 | |
| B | HIS167 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 16 |
| Details | BINDING: in chain C => ECO:0000269|PubMed:25267621, ECO:0007744|PDB:4TNQ |
| Chain | Residue | Details |
| A | VAL156 | |
| C | ARG372 | |
| C | HIS376 | |
| C | LYS377 | |
| D | VAL156 | |
| D | ARG372 | |
| D | HIS376 | |
| D | LYS377 | |
| A | ARG372 | |
| A | HIS376 | |
| A | LYS377 | |
| B | VAL156 | |
| B | ARG372 | |
| B | HIS376 | |
| B | LYS377 | |
| C | VAL156 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 12 |
| Details | BINDING: in chain A => ECO:0000269|PubMed:25267621, ECO:0007744|PDB:4TNQ |
| Chain | Residue | Details |
| A | ARG333 | |
| D | ARG333 | |
| D | ARG352 | |
| D | LYS354 | |
| A | ARG352 | |
| A | LYS354 | |
| B | ARG333 | |
| B | ARG352 | |
| B | LYS354 | |
| C | ARG333 | |
| C | ARG352 | |
| C | LYS354 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | BINDING: in chain A => ECO:0000269|PubMed:24141705, ECO:0000269|PubMed:25267621, ECO:0007744|PDB:4BZB, ECO:0007744|PDB:4TNX |
| Chain | Residue | Details |
| A | ASN358 | |
| B | ASN358 | |
| C | ASN358 | |
| D | ASN358 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 8 |
| Details | BINDING: in chain C => ECO:0000269|PubMed:25267621, ECO:0007744|PDB:4TNP, ECO:0007744|PDB:4TNQ, ECO:0007744|PDB:4TNR, ECO:0007744|PDB:4TNX |
| Chain | Residue | Details |
| A | ARG451 | |
| A | LYS455 | |
| B | ARG451 | |
| B | LYS455 | |
| C | ARG451 | |
| C | LYS455 | |
| D | ARG451 | |
| D | LYS455 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | BINDING: in chain A => ECO:0000269|PubMed:25267621, ECO:0007744|PDB:4TNP, ECO:0007744|PDB:4TNQ, ECO:0007744|PDB:4TNR, ECO:0007744|PDB:4TNX |
| Chain | Residue | Details |
| A | LYS523 | |
| B | LYS523 | |
| C | LYS523 | |
| D | LYS523 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine; by CDK1 => ECO:0000269|PubMed:23601106, ECO:0000269|PubMed:23602554, ECO:0000269|PubMed:26294762, ECO:0000269|PubMed:26431200, ECO:0000269|PubMed:29610582, ECO:0000269|PubMed:29670289, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:19369195, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | THR592 | |
| B | THR592 | |
| C | THR592 | |
| D | THR592 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 20 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS467 | |
| B | LYS622 | |
| C | LYS467 | |
| C | LYS469 | |
| C | LYS492 | |
| C | LYS622 | |
| D | LYS467 | |
| D | LYS469 | |
| D | LYS492 | |
| D | LYS622 | |
| A | LYS469 | |
| A | LYS492 | |
| A | LYS622 | |
| B | LYS467 | |
| B | LYS469 | |
| B | LYS492 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 12 |
| Details | M-CSA 994 |
| Chain | Residue | Details |
| A | GLN149 | hydrogen bond donor |
| A | LYS312 | hydrogen bond donor |
| A | ASP319 | hydrogen bond acceptor |
| A | ARG366 | hydrogen bond donor |
| A | HIS167 | metal ligand |
| A | HIS206 | metal ligand |
| A | ASP207 | metal ligand |
| A | HIS210 | hydrogen bond donor |
| A | HIS215 | electrostatic stabiliser, hydrogen bond donor, proton donor |
| A | ASP218 | electrostatic stabiliser, hydrogen bond acceptor |
| A | HIS233 | metal ligand |
| A | ASP311 | metal ligand |
