4DZ6
Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and adp
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 | 0005829 | cellular_component | cytosol |
A | 0006183 | biological_process | GTP biosynthetic process |
A | 0006228 | biological_process | UTP biosynthetic process |
A | 0006241 | biological_process | CTP biosynthetic process |
A | 0009117 | biological_process | nucleotide metabolic process |
A | 0016301 | molecular_function | kinase activity |
A | 0046872 | molecular_function | metal ion binding |
B | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
B | 0005524 | molecular_function | ATP binding |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0006183 | biological_process | GTP biosynthetic process |
B | 0006228 | biological_process | UTP biosynthetic process |
B | 0006241 | biological_process | CTP biosynthetic process |
B | 0009117 | biological_process | nucleotide metabolic process |
B | 0016301 | molecular_function | kinase activity |
B | 0046872 | molecular_function | metal ion binding |
C | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
C | 0005524 | molecular_function | ATP binding |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0006183 | biological_process | GTP biosynthetic process |
C | 0006228 | biological_process | UTP biosynthetic process |
C | 0006241 | biological_process | CTP biosynthetic process |
C | 0009117 | biological_process | nucleotide metabolic process |
C | 0016301 | molecular_function | kinase activity |
C | 0046872 | molecular_function | metal ion binding |
D | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
D | 0005524 | molecular_function | ATP binding |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0006183 | biological_process | GTP biosynthetic process |
D | 0006228 | biological_process | UTP biosynthetic process |
D | 0006241 | biological_process | CTP biosynthetic process |
D | 0009117 | biological_process | nucleotide metabolic process |
D | 0016301 | molecular_function | kinase activity |
D | 0046872 | molecular_function | metal ion binding |
E | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
E | 0005524 | molecular_function | ATP binding |
E | 0005737 | cellular_component | cytoplasm |
E | 0005829 | cellular_component | cytosol |
E | 0006183 | biological_process | GTP biosynthetic process |
E | 0006228 | biological_process | UTP biosynthetic process |
E | 0006241 | biological_process | CTP biosynthetic process |
E | 0009117 | biological_process | nucleotide metabolic process |
E | 0016301 | molecular_function | kinase activity |
E | 0046872 | molecular_function | metal ion binding |
F | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
F | 0005524 | molecular_function | ATP binding |
F | 0005737 | cellular_component | cytoplasm |
F | 0005829 | cellular_component | cytosol |
F | 0006183 | biological_process | GTP biosynthetic process |
F | 0006228 | biological_process | UTP biosynthetic process |
F | 0006241 | biological_process | CTP biosynthetic process |
F | 0009117 | biological_process | nucleotide metabolic process |
F | 0016301 | molecular_function | kinase activity |
F | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE ADP A 1001 |
Chain | Residue |
A | LYS13 |
A | ILE129 |
A | ASN131 |
A | VN41002 |
A | HOH1107 |
A | ARG61 |
A | HIS62 |
A | LEU70 |
A | ARG94 |
A | THR100 |
A | ARG111 |
A | PHE119 |
A | SER122 |
site_id | AC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE VN4 A 1002 |
Chain | Residue |
A | LYS13 |
A | TYR53 |
A | ARG94 |
A | ARG111 |
A | HIS134 |
A | ALA135 |
A | ADP1001 |
site_id | AC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE EDO A 1003 |
Chain | Residue |
A | LYS40 |
A | ILE148 |
A | TRP149 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE VO4 B 201 |
Chain | Residue |
B | LYS13 |
B | TYR53 |
B | ARG94 |
B | ARG111 |
B | HIS134 |
B | ALA135 |
site_id | AC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO B 202 |
Chain | Residue |
A | ASP162 |
A | HOH1114 |
B | ARG19 |
C | ARG19 |
E | ASP162 |
E | HOH328 |
site_id | AC6 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE ADP C 1001 |
Chain | Residue |
C | LYS13 |
C | ARG61 |
C | HIS62 |
C | LEU70 |
C | ARG94 |
C | THR100 |
C | ARG111 |
C | PHE119 |
C | SER122 |
C | SER128 |
C | ILE129 |
C | ASN131 |
C | VN41002 |
site_id | AC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE VN4 C 1002 |
Chain | Residue |
C | LYS13 |
C | TYR53 |
C | ARG94 |
C | ARG111 |
C | HIS134 |
C | ALA135 |
C | ADP1001 |
site_id | AC8 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE ADP D 1001 |
Chain | Residue |
D | LYS13 |
D | ARG61 |
D | HIS62 |
D | LEU70 |
D | ARG94 |
D | THR100 |
D | ARG111 |
D | PHE119 |
D | SER122 |
D | ASN123 |
D | SER128 |
D | ILE129 |
D | ASN131 |
D | VN41002 |
site_id | AC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE VN4 D 1002 |
Chain | Residue |
D | LYS13 |
D | TYR53 |
D | ARG111 |
D | HIS134 |
D | ALA135 |
D | ADP1001 |
site_id | BC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE VO4 E 201 |
Chain | Residue |
E | LYS13 |
E | TYR53 |
E | ARG94 |
E | ARG111 |
E | HIS134 |
E | ALA135 |
site_id | BC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE VO4 F 201 |
Chain | Residue |
F | LYS13 |
F | TYR53 |
F | ARG94 |
F | ARG111 |
F | HIS134 |
F | ALA135 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 6 |
Details | ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000250 |
Chain | Residue | Details |
A | HIS134 | |
B | HIS134 | |
C | HIS134 | |
D | HIS134 | |
E | HIS134 | |
F | HIS134 |
site_id | SWS_FT_FI2 |
Number of Residues | 30 |
Details | BINDING: BINDING => ECO:0000250 |
Chain | Residue | Details |
A | LYS13 | |
B | ASN131 | |
C | LYS13 | |
C | ARG94 | |
C | THR100 | |
C | ARG111 | |
C | ASN131 | |
D | LYS13 | |
D | ARG94 | |
D | THR100 | |
D | ARG111 | |
A | ARG94 | |
D | ASN131 | |
E | LYS13 | |
E | ARG94 | |
E | THR100 | |
E | ARG111 | |
E | ASN131 | |
F | LYS13 | |
F | ARG94 | |
F | THR100 | |
F | ARG111 | |
A | THR100 | |
F | ASN131 | |
A | ARG111 | |
A | ASN131 | |
B | LYS13 | |
B | ARG94 | |
B | THR100 | |
B | ARG111 |