5YPK
Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI2 complex
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0008800 | molecular_function | beta-lactamase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0017001 | biological_process | antibiotic catabolic process |
| A | 0042597 | cellular_component | periplasmic space |
| A | 0046677 | biological_process | response to antibiotic |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0008800 | molecular_function | beta-lactamase activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0017001 | biological_process | antibiotic catabolic process |
| B | 0042597 | cellular_component | periplasmic space |
| B | 0046677 | biological_process | response to antibiotic |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0008800 | molecular_function | beta-lactamase activity |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0017001 | biological_process | antibiotic catabolic process |
| C | 0042597 | cellular_component | periplasmic space |
| C | 0046677 | biological_process | response to antibiotic |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0008800 | molecular_function | beta-lactamase activity |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0017001 | biological_process | antibiotic catabolic process |
| D | 0042597 | cellular_component | periplasmic space |
| D | 0046677 | biological_process | response to antibiotic |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0008800 | molecular_function | beta-lactamase activity |
| E | 0016787 | molecular_function | hydrolase activity |
| E | 0017001 | biological_process | antibiotic catabolic process |
| E | 0042597 | cellular_component | periplasmic space |
| E | 0046677 | biological_process | response to antibiotic |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0008800 | molecular_function | beta-lactamase activity |
| F | 0016787 | molecular_function | hydrolase activity |
| F | 0017001 | biological_process | antibiotic catabolic process |
| F | 0042597 | cellular_component | periplasmic space |
| F | 0046677 | biological_process | response to antibiotic |
| F | 0046872 | molecular_function | metal ion binding |
| G | 0008800 | molecular_function | beta-lactamase activity |
| G | 0016787 | molecular_function | hydrolase activity |
| G | 0017001 | biological_process | antibiotic catabolic process |
| G | 0042597 | cellular_component | periplasmic space |
| G | 0046677 | biological_process | response to antibiotic |
| G | 0046872 | molecular_function | metal ion binding |
| H | 0008800 | molecular_function | beta-lactamase activity |
| H | 0016787 | molecular_function | hydrolase activity |
| H | 0017001 | biological_process | antibiotic catabolic process |
| H | 0042597 | cellular_component | periplasmic space |
| H | 0046677 | biological_process | response to antibiotic |
| H | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 301 |
| Chain | Residue |
| A | HIS120 |
| A | HIS122 |
| A | HIS189 |
| A | HIW303 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 302 |
| Chain | Residue |
| A | ASP124 |
| A | CYS208 |
| A | HIS250 |
| A | HIW303 |
| site_id | AC3 |
| Number of Residues | 15 |
| Details | binding site for residue HIW A 303 |
| Chain | Residue |
| A | HIS120 |
| A | HIS122 |
| A | ASP124 |
| A | HIS189 |
| A | CYS208 |
| A | LYS211 |
| A | GLY219 |
| A | ASN220 |
| A | HIS250 |
| A | ZN301 |
| A | ZN302 |
| A | HOH459 |
| H | GLY69 |
| H | PHE70 |
| A | TRP93 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 304 |
| Chain | Residue |
| A | ARG234 |
| A | THR260 |
| A | ARG264 |
| A | HOH407 |
| E | GLN44 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 301 |
| Chain | Residue |
| B | HIS120 |
| B | HIS122 |
| B | HIS189 |
| B | HIW303 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 302 |
| Chain | Residue |
| B | ASP124 |
| B | CYS208 |
| B | HIS250 |
| B | HIW303 |
| site_id | AC7 |
| Number of Residues | 15 |
| Details | binding site for residue HIW B 303 |
| Chain | Residue |
| B | TRP93 |
| B | HIS120 |
| B | HIS122 |
| B | GLN123 |
| B | ASP124 |
| B | HIS189 |
| B | CYS208 |
| B | LYS211 |
| B | GLY219 |
| B | ASN220 |
| B | HIS250 |
| B | ZN301 |
| B | ZN302 |
| B | HOH505 |
| B | HOH521 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 304 |
| Chain | Residue |
| B | ARG234 |
| B | THR260 |
| B | ARG264 |
| B | HOH436 |
| B | HOH502 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 301 |
| Chain | Residue |
| C | HIS120 |
| C | HIS122 |
| C | HIS189 |
| C | HIW303 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 302 |
| Chain | Residue |
| C | ASP124 |
| C | CYS208 |
| C | HIS250 |
| C | HIW303 |
| site_id | AD2 |
| Number of Residues | 15 |
| Details | binding site for residue HIW C 303 |
| Chain | Residue |
| C | HIS120 |
| C | HIS122 |
| C | ASP124 |
| C | HIS189 |
| C | CYS208 |
| C | LYS211 |
| C | SER217 |
| C | GLY219 |
| C | ASN220 |
| C | HIS250 |
| C | ZN301 |
| C | ZN302 |
| C | HOH416 |
| F | GLY69 |
| F | PHE70 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 304 |
| Chain | Residue |
| C | ARG234 |
| C | THR260 |
| C | ARG264 |
| C | HOH413 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 C 305 |
| Chain | Residue |
| C | GLN158 |
| C | HIS159 |
| C | SER160 |
| C | HOH404 |
| C | HOH509 |
| C | HOH531 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue NA C 306 |
| Chain | Residue |
| C | ASN166 |
| C | HOH545 |
| C | HOH559 |
| C | HOH590 |
| C | HOH636 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue NA C 307 |
| Chain | Residue |
| C | ARG45 |
| C | GLY47 |
| E | ASP48 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 301 |
| Chain | Residue |
| D | HIS189 |
| D | HIW303 |
| D | HIS120 |
| D | HIS122 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 302 |
| Chain | Residue |
| D | ASP124 |
| D | CYS208 |
| D | HIS250 |
| D | HIW303 |
| site_id | AD9 |
| Number of Residues | 16 |
| Details | binding site for residue HIW D 303 |
| Chain | Residue |
| D | TRP93 |
| D | HIS122 |
| D | ASP124 |
| D | HIS189 |
| D | CYS208 |
| D | LYS211 |
| D | SER217 |
| D | GLY219 |
| D | ASN220 |
| D | HIS250 |
| D | ZN301 |
| D | ZN302 |
| D | HOH406 |
| D | HOH569 |
| E | GLY69 |
| E | PHE70 |
| site_id | AE1 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 D 304 |
| Chain | Residue |
| D | ARG234 |
| D | ARG264 |
| H | GLN44 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for residue CL D 305 |
| Chain | Residue |
| D | HIS159 |
| D | SER160 |
| D | HOH440 |
| D | HOH547 |
| G | HOH452 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue NA D 306 |
| Chain | Residue |
| E | SER217 |
| E | HOH561 |
| E | HOH579 |
| site_id | AE4 |
| Number of Residues | 4 |
| Details | binding site for residue NA D 307 |
| Chain | Residue |
| D | GLN151 |
| D | HOH444 |
| D | HOH480 |
| F | PRO185 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue ZN E 301 |
| Chain | Residue |
| E | HIS120 |
| E | HIS122 |
| E | HIS189 |
| E | HIW303 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue ZN E 302 |
| Chain | Residue |
| E | ASP124 |
| E | CYS208 |
| E | HIS250 |
| E | HIW303 |
| site_id | AE7 |
| Number of Residues | 18 |
| Details | binding site for residue HIW E 303 |
| Chain | Residue |
| D | GLY69 |
| D | PHE70 |
| E | MET67 |
| E | VAL73 |
| E | TRP93 |
| E | HIS122 |
| E | ASP124 |
| E | HIS189 |
| E | CYS208 |
| E | LYS211 |
| E | LEU218 |
| E | GLY219 |
| E | ASN220 |
| E | HIS250 |
| E | ZN301 |
| E | ZN302 |
| E | HOH458 |
| E | HOH545 |
| site_id | AE8 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 E 304 |
| Chain | Residue |
| E | HIS261 |
| E | HOH410 |
| E | HOH418 |
| E | HOH419 |
| E | HOH459 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue NA E 305 |
| Chain | Residue |
| C | HOH513 |
| E | ASN166 |
| E | HOH482 |
| E | HOH599 |
| E | HOH600 |
| site_id | AF1 |
| Number of Residues | 5 |
| Details | binding site for residue ZN F 301 |
| Chain | Residue |
| F | HIS120 |
| F | HIS122 |
| F | HIS189 |
| F | HIW303 |
| F | HOH408 |
| site_id | AF2 |
| Number of Residues | 5 |
| Details | binding site for residue ZN F 302 |
| Chain | Residue |
| F | ASP124 |
| F | CYS208 |
| F | HIS250 |
| F | HIW303 |
| F | HOH408 |
| site_id | AF3 |
| Number of Residues | 14 |
| Details | binding site for residue HIW F 303 |
| Chain | Residue |
| C | GLY69 |
| C | PHE70 |
| F | HIS120 |
| F | HIS122 |
| F | GLN123 |
| F | ASP124 |
| F | HIS189 |
| F | CYS208 |
| F | LYS211 |
| F | ASN220 |
| F | HIS250 |
| F | ZN301 |
| F | ZN302 |
| F | HOH408 |
| site_id | AF4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 F 304 |
| Chain | Residue |
| B | HIS159 |
| F | HIS261 |
| F | ARG264 |
| F | HOH468 |
| site_id | AF5 |
| Number of Residues | 4 |
| Details | binding site for residue NA F 305 |
| Chain | Residue |
| F | HOH587 |
| F | HOH595 |
| F | HOH618 |
| F | HOH626 |
| site_id | AF6 |
| Number of Residues | 4 |
| Details | binding site for residue ZN G 301 |
| Chain | Residue |
| G | HIS120 |
| G | HIS122 |
| G | HIS189 |
| G | HIW303 |
| site_id | AF7 |
| Number of Residues | 4 |
| Details | binding site for residue ZN G 302 |
| Chain | Residue |
| G | ASP124 |
| G | CYS208 |
| G | HIS250 |
| G | HIW303 |
| site_id | AF8 |
| Number of Residues | 13 |
| Details | binding site for residue HIW G 303 |
| Chain | Residue |
| G | VAL73 |
| G | TRP93 |
| G | HIS120 |
| G | HIS122 |
| G | ASP124 |
| G | HIS189 |
| G | LYS211 |
| G | GLY219 |
| G | ASN220 |
| G | HIS250 |
| G | ZN301 |
| G | ZN302 |
| G | HOH402 |
| site_id | AF9 |
| Number of Residues | 5 |
| Details | binding site for residue NA G 304 |
| Chain | Residue |
| B | HIS228 |
| G | HIS122 |
| G | GLU152 |
| G | ASP223 |
| G | HOH525 |
| site_id | AG1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN H 301 |
| Chain | Residue |
| H | HIS120 |
| H | HIS122 |
| H | HIS189 |
| H | HIW303 |
| site_id | AG2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN H 302 |
| Chain | Residue |
| H | ASP124 |
| H | CYS208 |
| H | HIS250 |
| H | HIW303 |
| site_id | AG3 |
| Number of Residues | 18 |
| Details | binding site for residue HIW H 303 |
| Chain | Residue |
| A | GLY69 |
| A | PHE70 |
| A | HOH428 |
| H | TRP93 |
| H | HIS122 |
| H | GLN123 |
| H | ASP124 |
| H | HIS189 |
| H | CYS208 |
| H | LYS211 |
| H | SER217 |
| H | GLY219 |
| H | ASN220 |
| H | HIS250 |
| H | ZN301 |
| H | ZN302 |
| H | HOH419 |
| H | HOH425 |
