3F4N
Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0008615 | biological_process | pyridoxine biosynthetic process |
A | 0016740 | molecular_function | transferase activity |
A | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
A | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0008615 | biological_process | pyridoxine biosynthetic process |
B | 0016740 | molecular_function | transferase activity |
B | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
B | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0008615 | biological_process | pyridoxine biosynthetic process |
C | 0016740 | molecular_function | transferase activity |
C | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
C | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0008615 | biological_process | pyridoxine biosynthetic process |
D | 0016740 | molecular_function | transferase activity |
D | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
D | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
E | 0005737 | cellular_component | cytoplasm |
E | 0005829 | cellular_component | cytosol |
E | 0008615 | biological_process | pyridoxine biosynthetic process |
E | 0016740 | molecular_function | transferase activity |
E | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
E | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
F | 0005737 | cellular_component | cytoplasm |
F | 0005829 | cellular_component | cytosol |
F | 0008615 | biological_process | pyridoxine biosynthetic process |
F | 0016740 | molecular_function | transferase activity |
F | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
F | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
G | 0005737 | cellular_component | cytoplasm |
G | 0005829 | cellular_component | cytosol |
G | 0008615 | biological_process | pyridoxine biosynthetic process |
G | 0016740 | molecular_function | transferase activity |
G | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
G | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
H | 0005737 | cellular_component | cytoplasm |
H | 0005829 | cellular_component | cytosol |
H | 0008615 | biological_process | pyridoxine biosynthetic process |
H | 0016740 | molecular_function | transferase activity |
H | 0016769 | molecular_function | transferase activity, transferring nitrogenous groups |
H | 0033856 | molecular_function | pyridoxine 5'-phosphate synthase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE PXP A 501 |
Chain | Residue |
A | ASN9 |
A | GLY215 |
A | HIS216 |
A | HOH1046 |
A | HOH1177 |
A | HOH1353 |
A | HOH1439 |
B | ARG20 |
A | GLU72 |
A | VAL94 |
A | PHE133 |
A | GLU153 |
A | HIS193 |
A | GLY194 |
A | ASN213 |
A | ILE214 |
site_id | AC2 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PXP B 502 |
Chain | Residue |
A | ARG20 |
B | ASN9 |
B | GLU72 |
B | VAL94 |
B | PHE133 |
B | GLU153 |
B | HIS193 |
B | GLY194 |
B | ASN213 |
B | ILE214 |
B | GLY215 |
B | HIS216 |
B | HOH1048 |
B | HOH1091 |
B | HOH1312 |
site_id | AC3 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PXP C 503 |
Chain | Residue |
C | ASN9 |
C | GLU72 |
C | PHE133 |
C | GLU153 |
C | HIS193 |
C | GLY194 |
C | ASN213 |
C | ILE214 |
C | GLY215 |
C | HIS216 |
C | HOH1191 |
C | HOH1306 |
C | HOH1595 |
C | HOH1623 |
D | ARG20 |
site_id | AC4 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PXP D 504 |
Chain | Residue |
C | ARG20 |
D | GLU72 |
D | VAL94 |
D | PHE133 |
D | GLU153 |
D | HIS193 |
D | GLY194 |
D | ASN213 |
D | ILE214 |
D | GLY215 |
D | HIS216 |
D | HOH1001 |
D | HOH1184 |
D | HOH1214 |
D | HOH1581 |
site_id | AC5 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE PXP E 505 |
Chain | Residue |
E | ASN9 |
E | GLU72 |
E | PHE133 |
E | GLU153 |
E | HIS193 |
E | GLY194 |
E | ASN213 |
E | ILE214 |
E | GLY215 |
E | HIS216 |
E | HOH1083 |
E | HOH1567 |
E | HOH1626 |
F | ARG20 |
site_id | AC6 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PXP F 506 |
Chain | Residue |
E | ARG20 |
E | SO4602 |
F | GLU72 |
F | PHE133 |
F | GLU153 |
F | HIS193 |
F | GLY194 |
F | ASN213 |
F | ILE214 |
F | GLY215 |
F | HIS216 |
F | HOH1188 |
F | HOH1235 |
F | HOH1244 |
F | HOH1538 |
site_id | AC7 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PXP G 507 |
Chain | Residue |
G | HOH1352 |
G | HOH1518 |
G | HOH1519 |
G | HOH1617 |
G | HOH1627 |
H | ARG20 |
G | GLU72 |
G | PHE133 |
G | GLU153 |
G | HIS193 |
G | GLY194 |
G | ASN213 |
G | ILE214 |
G | GLY215 |
G | HIS216 |
site_id | AC8 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE PXP H 508 |
Chain | Residue |
G | ARG20 |
H | GLU72 |
H | VAL94 |
H | PHE133 |
H | GLU153 |
H | HIS193 |
H | GLY194 |
H | ASN213 |
H | ILE214 |
H | GLY215 |
H | HIS216 |
H | HOH1115 |
H | HOH1245 |
H | HOH1493 |
site_id | AC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 C 601 |
Chain | Residue |
C | HIS12 |
C | ARG47 |
C | ARG51 |
C | HIS52 |
C | HOH1191 |
C | HOH1624 |
D | ARG20 |
site_id | BC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 E 602 |
Chain | Residue |
E | ARG20 |
E | HOH1539 |
F | HIS12 |
F | HIS52 |
F | PXP506 |
F | HOH1389 |
F | HOH1556 |
site_id | BC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 E 603 |
Chain | Residue |
E | HIS12 |
E | ARG47 |
E | ARG51 |
E | HIS52 |
F | ARG20 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 16 |
Details | ACT_SITE: Proton acceptor => ECO:0000255|HAMAP-Rule:MF_00279 |
Chain | Residue | Details |
A | HIS45 | |
E | GLU72 | |
F | HIS45 | |
F | GLU72 | |
G | HIS45 | |
G | GLU72 | |
H | HIS45 | |
H | GLU72 | |
A | GLU72 | |
B | HIS45 | |
B | GLU72 | |
C | HIS45 | |
C | GLU72 | |
D | HIS45 | |
D | GLU72 | |
E | HIS45 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | ACT_SITE: Proton donor => ECO:0000255|HAMAP-Rule:MF_00279 |
Chain | Residue | Details |
A | HIS193 | |
B | HIS193 | |
C | HIS193 | |
D | HIS193 | |
E | HIS193 | |
F | HIS193 | |
G | HIS193 | |
H | HIS193 |
site_id | SWS_FT_FI3 |
Number of Residues | 64 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00279 |
Chain | Residue | Details |
A | ASN9 | |
B | ASP11 | |
B | ARG20 | |
B | ARG47 | |
B | HIS52 | |
B | THR102 | |
B | GLY194 | |
B | GLY215 | |
C | ASN9 | |
C | ASP11 | |
C | ARG20 | |
A | ASP11 | |
C | ARG47 | |
C | HIS52 | |
C | THR102 | |
C | GLY194 | |
C | GLY215 | |
D | ASN9 | |
D | ASP11 | |
D | ARG20 | |
D | ARG47 | |
D | HIS52 | |
A | ARG20 | |
D | THR102 | |
D | GLY194 | |
D | GLY215 | |
E | ASN9 | |
E | ASP11 | |
E | ARG20 | |
E | ARG47 | |
E | HIS52 | |
E | THR102 | |
E | GLY194 | |
A | ARG47 | |
E | GLY215 | |
F | ASN9 | |
F | ASP11 | |
F | ARG20 | |
F | ARG47 | |
F | HIS52 | |
F | THR102 | |
F | GLY194 | |
F | GLY215 | |
G | ASN9 | |
A | HIS52 | |
G | ASP11 | |
G | ARG20 | |
G | ARG47 | |
G | HIS52 | |
G | THR102 | |
G | GLY194 | |
G | GLY215 | |
H | ASN9 | |
H | ASP11 | |
H | ARG20 | |
A | THR102 | |
H | ARG47 | |
H | HIS52 | |
H | THR102 | |
H | GLY194 | |
H | GLY215 | |
A | GLY194 | |
A | GLY215 | |
B | ASN9 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | SITE: Transition state stabilizer => ECO:0000255|HAMAP-Rule:MF_00279 |
Chain | Residue | Details |
A | GLU153 | |
B | GLU153 | |
C | GLU153 | |
D | GLU153 | |
E | GLU153 | |
F | GLU153 | |
G | GLU153 | |
H | GLU153 |