3SHD
Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1
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 | 8 |
| Details | BINDING SITE FOR RESIDUE MN A 154 |
| Chain | Residue |
| A | GLU51 |
| A | GLU55 |
| A | MN155 |
| A | SO4156 |
| A | SO4157 |
| A | HOH160 |
| A | HOH162 |
| A | HOH163 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN A 155 |
| Chain | Residue |
| A | MN154 |
| A | SO4156 |
| A | HOH159 |
| A | HOH163 |
| A | HOH164 |
| A | HOH166 |
| A | GLU51 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE SO4 A 156 |
| Chain | Residue |
| A | ALA35 |
| A | GLY36 |
| A | HIS37 |
| A | GLU51 |
| A | MN154 |
| A | MN155 |
| A | SO4157 |
| A | HOH163 |
| A | HOH164 |
| A | HOH165 |
| A | HOH166 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SO4 A 157 |
| Chain | Residue |
| A | GLU23 |
| A | ASN32 |
| A | ALA35 |
| A | GLY36 |
| A | GLU51 |
| A | GLU55 |
| A | MN154 |
| A | SO4156 |
| A | SO4158 |
| A | HOH162 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 A 158 |
| Chain | Residue |
| A | THR7 |
| A | ASN32 |
| A | ALA35 |
| A | GLY36 |
| A | ARG81 |
| A | SO4157 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN B 154 |
| Chain | Residue |
| B | GLU51 |
| B | GLU55 |
| B | SO4156 |
| B | SO4157 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN B 155 |
| Chain | Residue |
| B | GLU51 |
| B | SO4156 |
| B | HOH177 |
| site_id | AC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 B 156 |
| Chain | Residue |
| B | GLY36 |
| B | HIS37 |
| B | GLU51 |
| B | MN154 |
| B | MN155 |
| B | SO4157 |
| B | HOH161 |
| B | HOH213 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 B 157 |
| Chain | Residue |
| B | GLU23 |
| B | ALA35 |
| B | GLY36 |
| B | GLU51 |
| B | GLU55 |
| B | MN154 |
| B | SO4156 |
| B | SO4158 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 B 158 |
| Chain | Residue |
| B | THR7 |
| B | ASN32 |
| B | ALA35 |
| B | GLY36 |
| B | ARG81 |
| B | SO4157 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN C 154 |
| Chain | Residue |
| C | GLU51 |
| C | GLU55 |
| C | MN155 |
| C | SO4156 |
| C | SO4157 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN C 155 |
| Chain | Residue |
| C | GLU51 |
| C | MN154 |
| C | SO4156 |
| C | HOH269 |
| site_id | BC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 C 156 |
| Chain | Residue |
| C | GLY36 |
| C | HIS37 |
| C | GLU51 |
| C | MN154 |
| C | MN155 |
| C | SO4157 |
| C | HOH250 |
| C | HOH269 |
| site_id | BC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 C 157 |
| Chain | Residue |
| C | GLU23 |
| C | ALA35 |
| C | GLY36 |
| C | GLU51 |
| C | GLU55 |
| C | MN154 |
| C | SO4156 |
| C | SO4158 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 C 158 |
| Chain | Residue |
| C | GLY36 |
| C | ARG81 |
| C | SO4157 |
| C | THR7 |
| C | ASN32 |
| C | ALA35 |
| site_id | BC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN D 154 |
| Chain | Residue |
| D | GLU51 |
| D | SO4156 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN D 155 |
| Chain | Residue |
| D | GLU51 |
| D | GLU55 |
| D | SO4156 |
| D | SO4157 |
| site_id | BC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 D 156 |
| Chain | Residue |
| D | GLY36 |
| D | HIS37 |
| D | GLU51 |
| D | GLU55 |
| D | MN154 |
| D | MN155 |
| D | SO4157 |
| D | HOH252 |
| site_id | CC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SO4 D 157 |
| Chain | Residue |
| D | GLU23 |
| D | ASN32 |
| D | ALA35 |
| D | GLY36 |
| D | GLU51 |
| D | GLU55 |
| D | ARG119 |
| D | MN155 |
| D | SO4156 |
| D | SO4158 |
| site_id | CC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 D 158 |
| Chain | Residue |
| D | THR7 |
| D | ASN32 |
| D | ALA35 |
| D | GLY36 |
| D | ARG81 |
| D | SO4157 |
| site_id | CC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN E 154 |
| Chain | Residue |
| E | GLU51 |
| E | MN155 |
| E | SO4156 |
| E | HOH172 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN E 155 |
| Chain | Residue |
| E | GLU51 |
| E | GLU55 |
| E | MN154 |
| E | SO4156 |
| E | SO4157 |
| site_id | CC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 E 156 |
| Chain | Residue |
| E | ALA35 |
| E | GLY36 |
| E | HIS37 |
| E | GLU51 |
| E | MN154 |
| E | MN155 |
| E | SO4157 |
| E | HOH171 |
| E | HOH172 |
| site_id | CC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 E 157 |
| Chain | Residue |
| E | GLU23 |
| E | ALA35 |
| E | GLY36 |
| E | GLU51 |
| E | GLU55 |
| E | MN155 |
| E | SO4156 |
| E | SO4158 |
| site_id | CC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 E 158 |
| Chain | Residue |
| E | THR7 |
| E | ASN32 |
| E | ALA35 |
| E | GLY36 |
| E | ARG81 |
| E | SO4157 |
| E | HOH235 |
| site_id | CC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN F 154 |
| Chain | Residue |
| F | GLU51 |
| F | GLU55 |
| F | MN155 |
| F | SO4156 |
| F | SO4157 |
| site_id | CC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN F 155 |
| Chain | Residue |
| F | GLU51 |
| F | MN154 |
| F | SO4156 |
| site_id | DC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 F 156 |
| Chain | Residue |
| F | GLY36 |
| F | HIS37 |
| F | GLU51 |
| F | MN154 |
| F | MN155 |
| F | SO4157 |
| site_id | DC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SO4 F 157 |
| Chain | Residue |
| F | GLU23 |
| F | ALA35 |
| F | GLY36 |
| F | GLU51 |
| F | GLU55 |
| F | ARG119 |
| F | MN154 |
| F | SO4156 |
| F | SO4158 |
| F | HOH169 |
| site_id | DC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 F 158 |
| Chain | Residue |
| F | THR7 |
| F | ASN32 |
| F | ALA35 |
| F | GLY36 |
| F | ARG81 |
| F | SO4157 |
| site_id | DC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN G 154 |
| Chain | Residue |
| G | GLU51 |
| G | GLU54 |
| G | GLU55 |
| G | MN155 |
| G | SO4156 |
| G | SO4158 |
| site_id | DC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN G 155 |
| Chain | Residue |
| G | GLU51 |
| G | MN154 |
| G | SO4156 |
| site_id | DC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 G 156 |
| Chain | Residue |
| G | GLY36 |
| G | HIS37 |
| G | GLU51 |
| G | MN154 |
| G | MN155 |
| G | SO4158 |
| site_id | DC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 G 157 |
| Chain | Residue |
| G | THR7 |
| G | ASN32 |
| G | ALA35 |
| G | GLY36 |
| G | ARG81 |
| G | SO4158 |
| site_id | DC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 G 158 |
| Chain | Residue |
| G | GLU23 |
| G | ALA35 |
| G | GLY36 |
| G | GLU51 |
| G | GLU55 |
| G | MN154 |
| G | SO4156 |
| G | SO4157 |
| G | HOH168 |
| site_id | DC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN H 154 |
| Chain | Residue |
| H | GLU51 |
| H | GLU55 |
| H | SO4156 |
| H | SO4157 |
| site_id | EC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN H 155 |
| Chain | Residue |
| H | GLU51 |
| H | SO4156 |
| site_id | EC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 H 156 |
| Chain | Residue |
| H | GLY36 |
| H | HIS37 |
| H | GLU51 |
| H | GLU55 |
| H | MN154 |
| H | MN155 |
| H | SO4157 |
| H | HOH160 |
| H | HOH162 |
| site_id | EC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 H 157 |
| Chain | Residue |
| H | GLU23 |
| H | ASN32 |
| H | ALA35 |
| H | GLY36 |
| H | GLU51 |
| H | GLU55 |
| H | MN154 |
| H | SO4156 |
| H | SO4158 |
| site_id | EC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 H 158 |
| Chain | Residue |
| H | THR7 |
| H | ASN32 |
| H | ALA35 |
| H | GLY36 |
| H | ARG81 |
| H | SO4157 |
| site_id | EC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN I 154 |
| Chain | Residue |
| I | GLU51 |
| I | GLU55 |
| I | MN155 |
| I | SO4156 |
| I | SO4157 |
| site_id | EC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN I 155 |
| Chain | Residue |
| I | ARG50 |
| I | GLU51 |
| I | GLU54 |
| I | MN154 |
| I | SO4156 |
| site_id | EC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 I 156 |
| Chain | Residue |
| I | HIS37 |
| I | GLU51 |
| I | MN154 |
| I | MN155 |
| I | SO4157 |
| site_id | EC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 I 157 |
| Chain | Residue |
| I | ALA35 |
| I | GLY36 |
| I | GLU55 |
| I | MN154 |
| I | SO4156 |
| I | SO4158 |
| site_id | EC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 I 158 |
| Chain | Residue |
| I | THR7 |
| I | ASN32 |
| I | ALA35 |
| I | ARG81 |
| I | SO4157 |
| site_id | FC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN J 154 |
| Chain | Residue |
| J | GLU51 |
| J | GLU55 |
| J | MN155 |
| J | SO4156 |
| J | SO4157 |
| site_id | FC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN J 155 |
| Chain | Residue |
| J | GLU51 |
| J | MN154 |
| J | SO4156 |
| J | HOH267 |
| site_id | FC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 J 156 |
| Chain | Residue |
| J | GLY36 |
| J | HIS37 |
| J | GLU51 |
| J | MN154 |
| J | MN155 |
| J | SO4157 |
| J | HOH175 |
| site_id | FC4 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 J 157 |
| Chain | Residue |
| J | GLU23 |
| J | ALA35 |
| J | GLY36 |
| J | GLU51 |
| J | GLU55 |
| J | MN154 |
| J | SO4156 |
| J | SO4158 |
| J | HOH175 |
| site_id | FC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 J 158 |
| Chain | Residue |
| J | THR7 |
| J | ASN32 |
| J | ALA35 |
| J | GLY36 |
| J | ARG81 |
| J | SO4157 |
| site_id | FC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MN K 154 |
| Chain | Residue |
| K | GLU51 |
| K | GLU55 |
| K | MN155 |
| K | SO4156 |
| K | SO4157 |
| K | HOH178 |
| K | HOH204 |
| site_id | FC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN K 155 |
| Chain | Residue |
| K | GLU51 |
| K | MN154 |
| K | SO4156 |
| site_id | FC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 K 156 |
| Chain | Residue |
| K | GLY36 |
| K | HIS37 |
| K | GLU51 |
| K | MN154 |
| K | MN155 |
| K | SO4157 |
| K | HOH172 |
| site_id | FC9 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SO4 K 157 |
| Chain | Residue |
| K | GLU23 |
| K | ASN32 |
| K | ALA35 |
| K | GLY36 |
| K | GLU51 |
| K | GLU55 |
| K | MN154 |
| K | SO4156 |
| K | SO4158 |
| K | HOH178 |
| site_id | GC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE SO4 K 158 |
| Chain | Residue |
| K | THR7 |
| K | ASN32 |
| K | ALA35 |
| K | GLY36 |
| K | ARG81 |
| K | SO4157 |
| site_id | GC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN L 154 |
| Chain | Residue |
| L | GLU51 |
| L | MN155 |
| L | SO4156 |
| site_id | GC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN L 155 |
| Chain | Residue |
| L | GLU51 |
| L | GLU54 |
| L | GLU55 |
| L | MN154 |
| L | SO4156 |
| L | SO4157 |
| site_id | GC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 L 156 |
| Chain | Residue |
| L | GLY36 |
| L | HIS37 |
| L | GLU51 |
| L | MN154 |
| L | MN155 |
| L | SO4157 |
| L | HOH173 |
| site_id | GC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 L 157 |
| Chain | Residue |
| L | GLU23 |
| L | ALA35 |
| L | GLY36 |
| L | GLU51 |
| L | GLU55 |
| L | MN155 |
| L | SO4156 |
| L | SO4158 |
| L | HOH173 |
| site_id | GC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 L 158 |
| Chain | Residue |
| L | THR7 |
| L | ASN32 |
| L | ARG81 |
| L | SO4157 |
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 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 988 |
| Chain | Residue | Details |
| I | GLU23 | electrostatic stabiliser |
| I | GLU51 | metal ligand |
| I | GLU55 | metal ligand |
| I | ARG119 | electrostatic stabiliser |
