2NV1
Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005515 | molecular_function | protein binding |
A | 0006520 | biological_process | amino acid metabolic process |
A | 0008615 | biological_process | pyridoxine biosynthetic process |
A | 0016829 | molecular_function | lyase activity |
A | 0016843 | molecular_function | amine-lyase activity |
A | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
A | 0042802 | molecular_function | identical protein binding |
A | 0042819 | biological_process | vitamin B6 biosynthetic process |
A | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
B | 0005515 | molecular_function | protein binding |
B | 0006520 | biological_process | amino acid metabolic process |
B | 0008615 | biological_process | pyridoxine biosynthetic process |
B | 0016829 | molecular_function | lyase activity |
B | 0016843 | molecular_function | amine-lyase activity |
B | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
B | 0042802 | molecular_function | identical protein binding |
B | 0042819 | biological_process | vitamin B6 biosynthetic process |
B | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
C | 0005515 | molecular_function | protein binding |
C | 0006520 | biological_process | amino acid metabolic process |
C | 0008615 | biological_process | pyridoxine biosynthetic process |
C | 0016829 | molecular_function | lyase activity |
C | 0016843 | molecular_function | amine-lyase activity |
C | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
C | 0042802 | molecular_function | identical protein binding |
C | 0042819 | biological_process | vitamin B6 biosynthetic process |
C | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
D | 0005515 | molecular_function | protein binding |
D | 0006520 | biological_process | amino acid metabolic process |
D | 0008615 | biological_process | pyridoxine biosynthetic process |
D | 0016829 | molecular_function | lyase activity |
D | 0016843 | molecular_function | amine-lyase activity |
D | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
D | 0042802 | molecular_function | identical protein binding |
D | 0042819 | biological_process | vitamin B6 biosynthetic process |
D | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
E | 0005515 | molecular_function | protein binding |
E | 0006520 | biological_process | amino acid metabolic process |
E | 0008615 | biological_process | pyridoxine biosynthetic process |
E | 0016829 | molecular_function | lyase activity |
E | 0016843 | molecular_function | amine-lyase activity |
E | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
E | 0042802 | molecular_function | identical protein binding |
E | 0042819 | biological_process | vitamin B6 biosynthetic process |
E | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
F | 0005515 | molecular_function | protein binding |
F | 0006520 | biological_process | amino acid metabolic process |
F | 0008615 | biological_process | pyridoxine biosynthetic process |
F | 0016829 | molecular_function | lyase activity |
F | 0016843 | molecular_function | amine-lyase activity |
F | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
F | 0042802 | molecular_function | identical protein binding |
F | 0042819 | biological_process | vitamin B6 biosynthetic process |
F | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CL A 3001 |
Chain | Residue |
A | ARG137 |
A | ARG138 |
A | HOH4103 |
A | HOH4214 |
A | HOH4328 |
site_id | AC2 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL A 3002 |
Chain | Residue |
A | GLY214 |
A | HOH4186 |
site_id | AC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG A 3003 |
Chain | Residue |
A | HOH4003 |
A | HOH4004 |
F | HOH4004 |
F | HOH4005 |
A | HOH4001 |
A | HOH4002 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG A 3004 |
Chain | Residue |
A | HOH4005 |
A | HOH4006 |
A | HOH4007 |
A | HOH4008 |
A | HOH4009 |
A | HOH4010 |
site_id | AC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL B 3007 |
Chain | Residue |
B | ARG137 |
B | ARG138 |
B | HOH4100 |
B | HOH4327 |
site_id | AC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL B 3008 |
Chain | Residue |
B | GLY153 |
B | GLY214 |
B | HOH4177 |
site_id | AC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG A 3009 |
Chain | Residue |
A | HOH4011 |
A | HOH4012 |
A | HOH4013 |
B | HOH4014 |
B | HOH4015 |
B | HOH4016 |
site_id | AC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG B 3010 |
Chain | Residue |
B | HOH4017 |
B | HOH4018 |
B | HOH4019 |
B | HOH4020 |
B | HOH4021 |
B | HOH4022 |
site_id | AC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL C 3013 |
Chain | Residue |
C | ARG137 |
C | ARG138 |
C | HOH4107 |
C | HOH4312 |
site_id | BC1 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE CL C 3014 |
Chain | Residue |
C | GLY214 |
site_id | BC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG C 3015 |
Chain | Residue |
B | HOH4023 |
B | HOH4024 |
C | HOH4026 |
C | HOH4027 |
C | HOH4028 |
C | HOH4029 |
site_id | BC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG C 3016 |
Chain | Residue |
C | HOH4030 |
C | HOH4031 |
C | HOH4032 |
C | HOH4033 |
C | HOH4034 |
C | HOH4035 |
site_id | BC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL D 3020 |
Chain | Residue |
D | ARG137 |
D | ARG138 |
D | HOH4113 |
D | HOH4411 |
site_id | BC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL D 3021 |
Chain | Residue |
D | GLY153 |
D | GLY214 |
D | HOH4128 |
D | HOH4171 |
site_id | BC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG C 3022 |
Chain | Residue |
C | HOH4036 |
C | HOH4037 |
C | HOH4038 |
D | HOH4038 |
D | HOH4039 |
D | HOH4040 |
site_id | BC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG D 3023 |
Chain | Residue |
D | HOH4041 |
D | HOH4042 |
D | HOH4043 |
D | HOH4044 |
D | HOH4045 |
D | HOH4046 |
site_id | BC8 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL E 3025 |
Chain | Residue |
E | ARG137 |
E | ARG138 |
E | HOH4141 |
site_id | BC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL E 3026 |
Chain | Residue |
E | GLY153 |
E | GLY214 |
E | HOH4190 |
E | HOH4428 |
site_id | CC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG D 3027 |
Chain | Residue |
D | HOH4047 |
D | HOH4048 |
E | HOH4049 |
E | HOH4050 |
E | HOH4051 |
E | HOH4052 |
site_id | CC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG E 3028 |
Chain | Residue |
E | HOH4053 |
E | HOH4054 |
E | HOH4055 |
E | HOH4056 |
E | HOH4057 |
E | HOH4058 |
site_id | CC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL F 3030 |
Chain | Residue |
F | ARG137 |
F | ARG138 |
F | HOH4096 |
site_id | CC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL F 3031 |
Chain | Residue |
F | HOH4254 |
F | GLY153 |
F | GLY214 |
site_id | CC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG E 3032 |
Chain | Residue |
E | HOH4059 |
E | HOH4060 |
E | HOH4061 |
F | HOH4006 |
F | HOH4007 |
F | HOH4008 |
site_id | CC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG F 3033 |
Chain | Residue |
F | HOH4009 |
F | HOH4010 |
F | HOH4011 |
F | HOH4012 |
F | HOH4013 |
F | HOH4014 |
site_id | CC7 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE EDO A 3005 |
Chain | Residue |
A | ALA186 |
A | LYS187 |
A | GLY190 |
A | ALA191 |
A | PRO192 |
A | PRO192 |
A | TYR193 |
A | HOH4334 |
A | HOH4334 |
site_id | CC8 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE EDO A 3006 |
Chain | Residue |
A | LYS187 |
A | LYS187 |
A | ASN188 |
A | GLY190 |
A | HOH4065 |
A | HOH4178 |
A | HOH4211 |
site_id | CC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO B 3011 |
Chain | Residue |
B | LYS187 |
B | HOH4347 |
F | LYS187 |
F | ASN188 |
F | LEU189 |
F | GLY190 |
site_id | DC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE EDO B 3012 |
Chain | Residue |
B | LYS187 |
B | ALA191 |
B | PRO192 |
B | TYR193 |
F | GLY190 |
F | PRO192 |
F | EDO3035 |
site_id | DC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE EDO C 3017 |
Chain | Residue |
C | PRO192 |
C | TYR193 |
C | GLU194 |
C | LEU195 |
C | HOH4139 |
C | HOH4214 |
E | PRO192 |
E | TYR193 |
E | GLU194 |
site_id | DC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE EDO C 3018 |
Chain | Residue |
C | ALA186 |
C | LYS187 |
C | ALA191 |
C | PRO192 |
C | TYR193 |
E | GLY190 |
E | PRO192 |
site_id | DC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE EDO C 3019 |
Chain | Residue |
C | ASP24 |
C | LYS81 |
C | ASP102 |
C | ARG147 |
C | PHE233 |
site_id | DC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE EDO D 3024 |
Chain | Residue |
D | ALA186 |
D | LYS187 |
D | GLY190 |
D | ALA191 |
D | PRO192 |
D | PRO192 |
D | TYR193 |
site_id | DC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO E 3029 |
Chain | Residue |
C | GLY190 |
C | PRO192 |
E | LYS187 |
E | ALA191 |
E | PRO192 |
E | TYR193 |
site_id | DC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE EDO F 3034 |
Chain | Residue |
B | PRO192 |
B | TYR193 |
B | GLU194 |
F | PRO192 |
F | TYR193 |
F | GLU194 |
F | LEU195 |
F | HOH4158 |
site_id | DC8 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE EDO F 3035 |
Chain | Residue |
B | GLY190 |
B | ALA191 |
B | PRO192 |
B | EDO3012 |
F | ALA186 |
F | LYS187 |
F | ALA191 |
F | PRO192 |
F | TYR193 |
Functional Information from PROSITE/UniProt
site_id | PS01235 |
Number of Residues | 19 |
Details | PDXS_SNZ_1 PdxS/SNZ family signature. LPVVNFAAGGVATPADAAL |
Chain | Residue | Details |
A | LEU205-LEU223 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 6 |
Details | ACT_SITE: Schiff-base intermediate with D-ribose 5-phosphate => ECO:0000255|HAMAP-Rule:MF_01824, ECO:0000269|PubMed:17189272 |
Chain | Residue | Details |
A | ALA82 | |
B | ALA82 | |
C | ALA82 | |
D | ALA82 | |
E | ALA82 | |
F | ALA82 |
site_id | SWS_FT_FI2 |
Number of Residues | 30 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01824 |
Chain | Residue | Details |
A | VAL25 | |
B | SER236 | |
C | VAL25 | |
C | THR154 | |
C | LYS166 | |
C | VAL215 | |
C | SER236 | |
D | VAL25 | |
D | THR154 | |
D | LYS166 | |
D | VAL215 | |
A | THR154 | |
D | SER236 | |
E | VAL25 | |
E | THR154 | |
E | LYS166 | |
E | VAL215 | |
E | SER236 | |
F | VAL25 | |
F | THR154 | |
F | LYS166 | |
F | VAL215 | |
A | LYS166 | |
F | SER236 | |
A | VAL215 | |
A | SER236 | |
B | VAL25 | |
B | THR154 | |
B | LYS166 | |
B | VAL215 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1g4p |
Chain | Residue | Details |
A | GLY128 |
site_id | CSA2 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1g4p |
Chain | Residue | Details |
B | GLY128 |
site_id | CSA3 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1g4p |
Chain | Residue | Details |
C | GLY128 |
site_id | CSA4 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1g4p |
Chain | Residue | Details |
D | GLY128 |
site_id | CSA5 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1g4p |
Chain | Residue | Details |
E | GLY128 |
site_id | CSA6 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1g4p |
Chain | Residue | Details |
F | GLY128 |