4NFW
Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| A | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| B | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| B | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| C | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| C | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| D | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| D | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| E | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| E | 0016787 | molecular_function | hydrolase activity |
| E | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| E | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| F | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| F | 0016787 | molecular_function | hydrolase activity |
| F | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| F | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| G | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| G | 0016787 | molecular_function | hydrolase activity |
| G | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| G | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| H | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| H | 0016787 | molecular_function | hydrolase activity |
| H | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| H | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| I | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| I | 0016787 | molecular_function | hydrolase activity |
| I | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| I | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| J | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| J | 0016787 | molecular_function | hydrolase activity |
| J | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| J | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| K | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| K | 0016787 | molecular_function | hydrolase activity |
| K | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| K | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
| L | 0004787 | molecular_function | thiamine diphosphate phosphatase activity |
| L | 0016787 | molecular_function | hydrolase activity |
| L | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| L | 0017111 | molecular_function | ribonucleoside triphosphate phosphatase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN A 201 |
| Chain | Residue |
| A | ALA35 |
| A | GLU51 |
| A | GLU55 |
| A | MN202 |
| A | SO4203 |
| A | SO4204 |
| A | HOH329 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN A 202 |
| Chain | Residue |
| A | SO4203 |
| A | HOH328 |
| A | HOH332 |
| A | HOH333 |
| A | HOH334 |
| A | GLU51 |
| A | MN201 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE SO4 A 203 |
| Chain | Residue |
| A | GLY36 |
| A | HIS37 |
| A | GLU51 |
| A | MN201 |
| A | MN202 |
| A | SO4204 |
| A | HOH331 |
| A | HOH332 |
| A | HOH333 |
| A | HOH334 |
| A | HOH335 |
| A | HOH337 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 A 204 |
| Chain | Residue |
| A | GLU23 |
| A | ASN32 |
| A | ALA35 |
| A | GLY36 |
| A | GLU55 |
| A | MN201 |
| A | SO4203 |
| A | SO4205 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 205 |
| Chain | Residue |
| A | THR7 |
| A | ASN32 |
| A | ALA35 |
| A | ARG81 |
| A | SO4204 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN B 201 |
| Chain | Residue |
| B | GLU51 |
| B | GLU54 |
| B | GLU55 |
| B | ASP98 |
| B | MN202 |
| B | SO4203 |
| B | SO4204 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN B 202 |
| Chain | Residue |
| B | GLU51 |
| B | MN201 |
| B | SO4203 |
| B | HOH308 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 B 203 |
| Chain | Residue |
| B | GLY36 |
| B | HIS37 |
| B | MN201 |
| B | MN202 |
| B | SO4204 |
| B | HOH304 |
| B | HOH319 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 B 204 |
| Chain | Residue |
| B | GLU23 |
| B | ASN32 |
| B | ALA35 |
| B | GLU55 |
| B | MN201 |
| B | SO4203 |
| B | SO4205 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 B 205 |
| Chain | Residue |
| B | THR7 |
| B | ASN32 |
| B | ALA35 |
| B | ARG81 |
| B | SO4204 |
| site_id | BC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN C 201 |
| Chain | Residue |
| C | GLU51 |
| C | GLU54 |
| C | GLU55 |
| C | ASP98 |
| C | MN202 |
| C | SO4203 |
| C | SO4204 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN C 202 |
| Chain | Residue |
| C | GLU39 |
| C | ARG50 |
| C | GLU51 |
| C | MN201 |
| C | SO4203 |
| C | HOH327 |
| site_id | BC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 C 203 |
| Chain | Residue |
| C | GLY36 |
| C | HIS37 |
| C | GLU51 |
| C | MN201 |
| C | MN202 |
| C | SO4204 |
| C | HOH303 |
| site_id | BC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 C 204 |
| Chain | Residue |
| C | GLU23 |
| C | ALA35 |
| C | GLY36 |
| C | GLU51 |
| C | GLU55 |
| C | MN201 |
| C | SO4203 |
| C | SO4205 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 C 205 |
| Chain | Residue |
| C | ALA35 |
| C | ARG81 |
| C | SO4204 |
| C | HOH329 |
| C | THR7 |
| C | ASN32 |
| site_id | BC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN D 201 |
| Chain | Residue |
| D | GLU39 |
| D | GLU51 |
| D | SO4203 |
| site_id | BC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN D 202 |
| Chain | Residue |
| D | GLU51 |
| D | GLU54 |
| D | GLU55 |
| D | SO4203 |
| D | SO4204 |
| site_id | BC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 D 203 |
| Chain | Residue |
| D | GLY36 |
| D | HIS37 |
| D | GLU51 |
| D | MN201 |
| D | MN202 |
| D | SO4204 |
| site_id | CC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 D 204 |
| Chain | Residue |
| D | GLU23 |
| D | ASN32 |
| D | ALA35 |
| D | GLY36 |
| D | GLU55 |
| D | ARG119 |
| D | MN202 |
| D | SO4203 |
| D | SO4205 |
| site_id | CC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 D 205 |
| Chain | Residue |
| D | THR7 |
| D | ASN32 |
| D | ALA35 |
| D | ARG81 |
| D | SO4204 |
| D | HOH322 |
| site_id | CC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN E 201 |
| Chain | Residue |
| E | GLU39 |
| E | GLU51 |
| E | MN202 |
| E | SO4203 |
| E | HOH304 |
| site_id | CC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN E 202 |
| Chain | Residue |
| E | GLU51 |
| E | GLU55 |
| E | ASP98 |
| E | MN201 |
| E | SO4203 |
| E | SO4204 |
| site_id | CC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 E 203 |
| Chain | Residue |
| E | ALA35 |
| E | GLY36 |
| E | HIS37 |
| E | MN201 |
| E | MN202 |
| E | SO4204 |
| E | HOH304 |
| E | HOH312 |
| site_id | CC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 E 204 |
| Chain | Residue |
| E | GLU23 |
| E | ALA35 |
| E | GLY36 |
| E | GLU55 |
| E | MN202 |
| E | SO4203 |
| E | SO4205 |
| site_id | CC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 E 205 |
| Chain | Residue |
| E | THR7 |
| E | ASN32 |
| E | ALA35 |
| E | ARG81 |
| E | SO4204 |
| E | HOH326 |
| site_id | CC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN F 201 |
| Chain | Residue |
| F | ALA35 |
| F | GLU51 |
| F | GLU55 |
| F | MN202 |
| F | SO4203 |
| F | SO4204 |
| site_id | CC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN F 202 |
| Chain | Residue |
| F | GLU51 |
| F | MN201 |
| F | SO4203 |
| site_id | DC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 F 203 |
| Chain | Residue |
| F | GLY36 |
| F | HIS37 |
| F | MN201 |
| F | MN202 |
| F | SO4204 |
| site_id | DC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 F 204 |
| Chain | Residue |
| F | GLU23 |
| F | ASN32 |
| F | ALA35 |
| F | GLY36 |
| F | GLU55 |
| F | ARG119 |
| F | MN201 |
| F | SO4203 |
| F | SO4205 |
| site_id | DC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 F 205 |
| Chain | Residue |
| F | THR7 |
| F | ASN32 |
| F | ALA35 |
| F | ARG81 |
| F | SO4204 |
| site_id | DC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN G 201 |
| Chain | Residue |
| G | GLU51 |
| G | GLU55 |
| G | SO4203 |
| G | SO4205 |
| site_id | DC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN G 202 |
| Chain | Residue |
| G | GLU51 |
| G | SO4203 |
| site_id | DC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 G 203 |
| Chain | Residue |
| G | GLY36 |
| G | HIS37 |
| G | GLU51 |
| G | MN201 |
| G | MN202 |
| G | SO4205 |
| G | HOH310 |
| site_id | DC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 G 204 |
| Chain | Residue |
| G | THR7 |
| G | ASN32 |
| G | PHE79 |
| G | ARG81 |
| G | SO4205 |
| site_id | DC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 G 205 |
| Chain | Residue |
| G | GLU23 |
| G | ASN32 |
| G | ALA35 |
| G | GLU55 |
| G | MN201 |
| G | SO4203 |
| G | SO4204 |
| site_id | DC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN H 201 |
| Chain | Residue |
| H | GLU51 |
| H | GLU55 |
| H | ASP98 |
| H | MN202 |
| H | SO4203 |
| H | SO4204 |
| site_id | EC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN H 202 |
| Chain | Residue |
| H | GLU51 |
| H | MN201 |
| H | SO4203 |
| site_id | EC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 H 203 |
| Chain | Residue |
| H | GLY36 |
| H | HIS37 |
| H | MN201 |
| H | MN202 |
| H | SO4204 |
| H | HOH302 |
| H | HOH305 |
| site_id | EC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 H 204 |
| Chain | Residue |
| H | ASN32 |
| H | ALA35 |
| H | GLY36 |
| H | GLU55 |
| H | MN201 |
| H | SO4203 |
| H | SO4205 |
| H | HOH305 |
| site_id | EC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 H 205 |
| Chain | Residue |
| H | THR7 |
| H | ASN32 |
| H | ALA35 |
| H | GLY36 |
| H | ARG81 |
| H | SO4204 |
| H | HOH320 |
| site_id | EC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 201 |
| Chain | Residue |
| I | GLU51 |
| I | SO4202 |
| site_id | EC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 I 202 |
| Chain | Residue |
| I | HIS37 |
| I | GLU51 |
| I | MN201 |
| site_id | EC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 I 203 |
| Chain | Residue |
| I | ALA35 |
| I | GLY36 |
| I | ARG119 |
| site_id | EC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN J 201 |
| Chain | Residue |
| J | ALA35 |
| J | GLU51 |
| J | GLU55 |
| J | SO4203 |
| J | SO4204 |
| site_id | EC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN J 202 |
| Chain | Residue |
| J | HIS37 |
| J | GLU51 |
| J | SO4203 |
| J | HOH310 |
| site_id | FC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 J 203 |
| Chain | Residue |
| J | GLY36 |
| J | HIS37 |
| J | GLU51 |
| J | MN201 |
| J | MN202 |
| J | SO4204 |
| J | HOH308 |
| site_id | FC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 J 204 |
| Chain | Residue |
| J | GLU23 |
| J | ALA35 |
| J | GLY36 |
| J | GLU55 |
| J | ARG119 |
| J | MN201 |
| J | SO4203 |
| J | SO4205 |
| J | HOH308 |
| site_id | FC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 J 205 |
| Chain | Residue |
| J | THR7 |
| J | ASN32 |
| J | ARG81 |
| J | SO4204 |
| site_id | FC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN K 201 |
| Chain | Residue |
| K | ALA35 |
| K | GLU51 |
| K | GLU55 |
| K | MN202 |
| K | SO4203 |
| K | SO4204 |
| K | HOH312 |
| site_id | FC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN K 202 |
| Chain | Residue |
| K | GLU51 |
| K | MN201 |
| K | SO4203 |
| site_id | FC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 K 203 |
| Chain | Residue |
| K | GLY36 |
| K | HIS37 |
| K | MN201 |
| K | MN202 |
| K | SO4204 |
| K | HOH310 |
| site_id | FC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 K 204 |
| Chain | Residue |
| K | GLU23 |
| K | ASN32 |
| K | ALA35 |
| K | GLY36 |
| K | GLU51 |
| K | GLU55 |
| K | MN201 |
| K | SO4203 |
| K | SO4205 |
| site_id | FC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 K 205 |
| Chain | Residue |
| K | THR7 |
| K | ASN32 |
| K | ALA35 |
| K | GLY36 |
| K | ARG81 |
| K | SO4204 |
| site_id | FC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN L 201 |
| Chain | Residue |
| L | GLU51 |
| L | SO4202 |
| site_id | GC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 L 202 |
| Chain | Residue |
| L | HIS37 |
| L | MN201 |
| L | SO4203 |
| site_id | GC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 L 203 |
| Chain | Residue |
| L | GLU23 |
| L | ALA35 |
| L | GLY36 |
| L | GLU51 |
| L | GLU55 |
| L | SO4202 |
| L | SO4204 |
| site_id | GC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 L 204 |
| Chain | Residue |
| L | THR7 |
| L | ASN32 |
| L | ALA35 |
| L | GLY36 |
| L | SO4203 |
Functional Information from PROSITE/UniProt
| site_id | PS00893 |
| Number of Residues | 22 |
| Details | NUDIX_BOX Nudix box signature. GhleadEtlveAAaRELwEEtG |
| Chain | Residue | Details |
| A | GLY36-GLY57 |
