2BEF
CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
A | 0005524 | molecular_function | ATP binding |
A | 0005737 | cellular_component | cytoplasm |
A | 0005840 | cellular_component | ribosome |
A | 0005856 | cellular_component | cytoskeleton |
A | 0005886 | cellular_component | plasma membrane |
A | 0006183 | biological_process | GTP biosynthetic process |
A | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
A | 0006228 | biological_process | UTP biosynthetic process |
A | 0006241 | biological_process | CTP biosynthetic process |
A | 0006414 | biological_process | translational elongation |
A | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
A | 0009117 | biological_process | nucleotide metabolic process |
A | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
A | 0009617 | biological_process | response to bacterium |
A | 0015629 | cellular_component | actin cytoskeleton |
A | 0016301 | molecular_function | kinase activity |
A | 0019954 | biological_process | asexual reproduction |
A | 0030036 | biological_process | actin cytoskeleton organization |
A | 0030141 | cellular_component | secretory granule |
A | 0045335 | cellular_component | phagocytic vesicle |
A | 0045920 | biological_process | negative regulation of exocytosis |
A | 0046872 | molecular_function | metal ion binding |
A | 0048550 | biological_process | negative regulation of pinocytosis |
A | 0050765 | biological_process | negative regulation of phagocytosis |
B | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
B | 0005524 | molecular_function | ATP binding |
B | 0005737 | cellular_component | cytoplasm |
B | 0005840 | cellular_component | ribosome |
B | 0005856 | cellular_component | cytoskeleton |
B | 0005886 | cellular_component | plasma membrane |
B | 0006183 | biological_process | GTP biosynthetic process |
B | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
B | 0006228 | biological_process | UTP biosynthetic process |
B | 0006241 | biological_process | CTP biosynthetic process |
B | 0006414 | biological_process | translational elongation |
B | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
B | 0009117 | biological_process | nucleotide metabolic process |
B | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
B | 0009617 | biological_process | response to bacterium |
B | 0015629 | cellular_component | actin cytoskeleton |
B | 0016301 | molecular_function | kinase activity |
B | 0019954 | biological_process | asexual reproduction |
B | 0030036 | biological_process | actin cytoskeleton organization |
B | 0030141 | cellular_component | secretory granule |
B | 0045335 | cellular_component | phagocytic vesicle |
B | 0045920 | biological_process | negative regulation of exocytosis |
B | 0046872 | molecular_function | metal ion binding |
B | 0048550 | biological_process | negative regulation of pinocytosis |
B | 0050765 | biological_process | negative regulation of phagocytosis |
C | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
C | 0005524 | molecular_function | ATP binding |
C | 0005737 | cellular_component | cytoplasm |
C | 0005840 | cellular_component | ribosome |
C | 0005856 | cellular_component | cytoskeleton |
C | 0005886 | cellular_component | plasma membrane |
C | 0006183 | biological_process | GTP biosynthetic process |
C | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
C | 0006228 | biological_process | UTP biosynthetic process |
C | 0006241 | biological_process | CTP biosynthetic process |
C | 0006414 | biological_process | translational elongation |
C | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
C | 0009117 | biological_process | nucleotide metabolic process |
C | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
C | 0009617 | biological_process | response to bacterium |
C | 0015629 | cellular_component | actin cytoskeleton |
C | 0016301 | molecular_function | kinase activity |
C | 0019954 | biological_process | asexual reproduction |
C | 0030036 | biological_process | actin cytoskeleton organization |
C | 0030141 | cellular_component | secretory granule |
C | 0045335 | cellular_component | phagocytic vesicle |
C | 0045920 | biological_process | negative regulation of exocytosis |
C | 0046872 | molecular_function | metal ion binding |
C | 0048550 | biological_process | negative regulation of pinocytosis |
C | 0050765 | biological_process | negative regulation of phagocytosis |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 156 |
Chain | Residue |
A | BEF157 |
A | ADP158 |
A | HOH619 |
A | HOH626 |
A | HOH693 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG B 156 |
Chain | Residue |
B | HOH779 |
B | BEF157 |
B | ADP158 |
B | HOH620 |
B | HOH706 |
site_id | AC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG C 156 |
Chain | Residue |
C | BEF157 |
C | ADP158 |
C | HOH643 |
C | HOH777 |
C | HOH778 |
site_id | AC4 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE BEF A 157 |
Chain | Residue |
A | LYS16 |
A | TYR56 |
A | ARG92 |
A | ARG109 |
A | HIS122 |
A | GLY123 |
A | MG156 |
A | ADP158 |
A | HOH619 |
A | HOH626 |
site_id | AC5 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE ADP A 158 |
Chain | Residue |
A | LYS16 |
A | HIS59 |
A | PHE64 |
A | LEU68 |
A | ARG92 |
A | THR98 |
A | ARG109 |
A | VAL116 |
A | ASN119 |
A | MG156 |
A | BEF157 |
A | HOH619 |
A | HOH626 |
A | HOH681 |
A | HOH693 |
A | HOH729 |
site_id | AC6 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE BEF B 157 |
Chain | Residue |
B | LYS16 |
B | TYR56 |
B | ARG92 |
B | ARG109 |
B | HIS122 |
B | GLY123 |
B | MG156 |
B | ADP158 |
B | HOH620 |
B | HOH779 |
site_id | AC7 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE ADP B 158 |
Chain | Residue |
A | LYS60 |
B | LYS16 |
B | HIS59 |
B | PHE64 |
B | LEU68 |
B | ARG92 |
B | THR98 |
B | ARG109 |
B | VAL116 |
B | ASN119 |
B | MG156 |
B | BEF157 |
B | HOH706 |
B | HOH779 |
B | HOH802 |
site_id | AC8 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE BEF C 157 |
Chain | Residue |
C | LYS16 |
C | TYR56 |
C | ARG109 |
C | HIS122 |
C | GLY123 |
C | MG156 |
C | ADP158 |
C | HOH643 |
C | HOH777 |
site_id | AC9 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE ADP C 158 |
Chain | Residue |
C | LYS16 |
C | TYR56 |
C | HIS59 |
C | PHE64 |
C | LEU68 |
C | ARG92 |
C | THR98 |
C | ARG109 |
C | VAL116 |
C | ASN119 |
C | MG156 |
C | BEF157 |
C | HOH617 |
C | HOH643 |
C | HOH778 |
Functional Information from PROSITE/UniProt
site_id | PS00469 |
Number of Residues | 9 |
Details | NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NiiHGSDSV |
Chain | Residue | Details |
A | ASN119-VAL127 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 3 |
Details | ACT_SITE: Pros-phosphohistidine intermediate |
Chain | Residue | Details |
A | HIS122 | |
B | HIS122 | |
C | HIS122 |
site_id | SWS_FT_FI2 |
Number of Residues | 18 |
Details | BINDING: |
Chain | Residue | Details |
A | LYS16 | |
B | THR98 | |
B | ARG109 | |
B | ASN119 | |
C | LYS16 | |
C | PHE64 | |
C | ARG92 | |
C | THR98 | |
C | ARG109 | |
C | ASN119 | |
A | PHE64 | |
A | ARG92 | |
A | THR98 | |
A | ARG109 | |
A | ASN119 | |
B | LYS16 | |
B | PHE64 | |
B | ARG92 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1nsp |
Chain | Residue | Details |
A | ASN119 | |
A | LYS16 |
site_id | CSA2 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1nsp |
Chain | Residue | Details |
B | ASN119 | |
B | LYS16 |
site_id | CSA3 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1nsp |
Chain | Residue | Details |
C | ASN119 | |
C | LYS16 |
site_id | CSA4 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1nsp |
Chain | Residue | Details |
A | TYR56 | |
A | LYS16 |
site_id | CSA5 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1nsp |
Chain | Residue | Details |
B | TYR56 | |
B | LYS16 |
site_id | CSA6 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1nsp |
Chain | Residue | Details |
C | TYR56 | |
C | LYS16 |
site_id | MCSA1 |
Number of Residues | 5 |
Details | M-CSA 150 |
Chain | Residue | Details |
A | LYS16 | electrostatic stabiliser, hydrogen bond donor |
A | TYR56 | electrostatic stabiliser, hydrogen bond donor |
A | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
A | HIS122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
A | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
site_id | MCSA2 |
Number of Residues | 5 |
Details | M-CSA 150 |
Chain | Residue | Details |
B | LYS16 | electrostatic stabiliser, hydrogen bond donor |
B | TYR56 | electrostatic stabiliser, hydrogen bond donor |
B | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
B | HIS122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
B | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
site_id | MCSA3 |
Number of Residues | 5 |
Details | M-CSA 150 |
Chain | Residue | Details |
C | LYS16 | electrostatic stabiliser, hydrogen bond donor |
C | TYR56 | electrostatic stabiliser, hydrogen bond donor |
C | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
C | HIS122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
C | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |