5YJW
Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with the competitive inhibitor, stigmatellin.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003954 | molecular_function | NADH dehydrogenase activity |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005743 | cellular_component | mitochondrial inner membrane |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0006120 | biological_process | mitochondrial electron transport, NADH to ubiquinone |
| A | 0015980 | biological_process | energy derivation by oxidation of organic compounds |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0043065 | biological_process | positive regulation of apoptotic process |
| A | 0050136 | molecular_function | NADH dehydrogenase (quinone) (non-electrogenic) activity |
| A | 0120555 | molecular_function | NADH dehydrogenase (ubiquinone) (non-electrogenic) activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 41 |
| Details | binding site for residue FAD A 601 |
| Chain | Residue |
| A | GLY60 |
| A | THR91 |
| A | PRO92 |
| A | GLU128 |
| A | ALA129 |
| A | ALA175 |
| A | VAL176 |
| A | GLY177 |
| A | LEU195 |
| A | THR239 |
| A | ARG344 |
| A | SER61 |
| A | GLY382 |
| A | ASP383 |
| A | PRO391 |
| A | THR392 |
| A | ALA393 |
| A | GLN394 |
| A | TYR482 |
| A | MG602 |
| A | MG603 |
| A | MG604 |
| A | GLY62 |
| A | MG605 |
| A | GOL608 |
| A | PEG615 |
| A | MES623 |
| A | SMA626 |
| A | HOH702 |
| A | HOH703 |
| A | HOH706 |
| A | HOH736 |
| A | HOH826 |
| A | TRP63 |
| A | HOH832 |
| A | HOH925 |
| A | GLY64 |
| A | ILE82 |
| A | SER83 |
| A | PRO84 |
| A | ARG85 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue MG A 602 |
| Chain | Residue |
| A | ALA175 |
| A | GLY177 |
| A | ILE381 |
| A | GLY382 |
| A | ASP383 |
| A | ASN384 |
| A | FAD601 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 603 |
| Chain | Residue |
| A | GLY62 |
| A | GLY64 |
| A | ALA65 |
| A | ALA175 |
| A | FAD601 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 604 |
| Chain | Residue |
| A | ARG85 |
| A | THR91 |
| A | FAD601 |
| A | HOH731 |
| A | HOH832 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 605 |
| Chain | Residue |
| A | GLY177 |
| A | ALA178 |
| A | LYS196 |
| A | ASP383 |
| A | FAD601 |
| A | HOH703 |
| site_id | AC6 |
| Number of Residues | 16 |
| Details | binding site for residue PE4 A 606 |
| Chain | Residue |
| A | PRO37 |
| A | SER39 |
| A | PHE40 |
| A | VAL112 |
| A | ASN113 |
| A | LEU212 |
| A | ASN216 |
| A | TYR250 |
| A | PHE258 |
| A | LEU259 |
| A | ARG490 |
| A | ASP508 |
| A | PHE509 |
| A | PHE510 |
| A | HOH729 |
| A | HOH735 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue P6G A 607 |
| Chain | Residue |
| A | GLU433 |
| A | ALA503 |
| A | SMA625 |
| site_id | AC8 |
| Number of Residues | 10 |
| Details | binding site for residue GOL A 608 |
| Chain | Residue |
| A | PRO238 |
| A | THR392 |
| A | ALA446 |
| A | LEU447 |
| A | FAD601 |
| A | MES623 |
| A | SMA626 |
| A | HOH860 |
| A | HOH925 |
| A | HOH943 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 609 |
| Chain | Residue |
| A | SER360 |
| A | LYS361 |
| A | ARG362 |
| A | GLY363 |
| A | ALA365 |
| A | PHE386 |
| site_id | AD1 |
| Number of Residues | 8 |
| Details | binding site for residue GOL A 610 |
| Chain | Residue |
| A | LEU202 |
| A | ARG206 |
| A | LYS511 |
| A | GLY512 |
| A | GLY512 |
| A | LEU513 |
| A | HOH805 |
| A | HOH805 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 611 |
| Chain | Residue |
| A | ARG303 |
| A | THR304 |
| A | ALA305 |
| A | LYS317 |
| A | LYS319 |
| A | HOH891 |
| site_id | AD3 |
| Number of Residues | 7 |
| Details | binding site for residue PG4 A 612 |
| Chain | Residue |
| A | THR38 |
| A | PRO84 |
| A | ARG85 |
| A | SER86 |
| A | TYR87 |
| A | GOL622 |
| A | HOH714 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue PG4 A 613 |
| Chain | Residue |
| A | ASP52 |
| A | ASP170 |
| A | ASN377 |
| A | PHE416 |
| A | GLN417 |
| A | LYS418 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue PEG A 614 |
| Chain | Residue |
| A | PRO48 |
| A | TYR288 |
| A | GLY469 |
| A | GLY470 |
| A | HOH842 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue PEG A 615 |
| Chain | Residue |
| A | ARG344 |
| A | PRO345 |
| A | VAL346 |
| A | FAD601 |
| A | HOH726 |
| site_id | AD7 |
| Number of Residues | 1 |
| Details | binding site for residue PGE A 616 |
| Chain | Residue |
| A | SMA626 |
| site_id | AD8 |
| Number of Residues | 2 |
| Details | binding site for residue PGE A 617 |
| Chain | Residue |
| A | ARG492 |
| A | PGE619 |
| site_id | AD9 |
| Number of Residues | 8 |
| Details | binding site for residue PEG A 618 |
| Chain | Residue |
| A | ILE185 |
| A | VAL234 |
| A | VAL271 |
| A | ALA273 |
| A | THR304 |
| A | VAL306 |
| A | HOH822 |
| A | HOH848 |
| site_id | AE1 |
| Number of Residues | 3 |
| Details | binding site for residue PGE A 619 |
| Chain | Residue |
| A | PHE504 |
| A | PGE617 |
| A | HOH759 |
| site_id | AE2 |
| Number of Residues | 10 |
| Details | binding site for residue GOL A 620 |
| Chain | Residue |
| A | ASP249 |
| A | GLN253 |
| A | TYR449 |
| A | GLU453 |
| A | ARG479 |
| A | LEU502 |
| A | ARG507 |
| A | HOH716 |
| A | HOH749 |
| A | HOH753 |
| site_id | AE3 |
| Number of Residues | 10 |
| Details | binding site for residue GOL A 621 |
| Chain | Residue |
| A | GLY236 |
| A | GLY237 |
| A | GLU272 |
| A | ILE276 |
| A | VAL277 |
| A | LEU278 |
| A | ASN279 |
| A | MET280 |
| A | HOH707 |
| A | HOH807 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 622 |
| Chain | Residue |
| A | PRO84 |
| A | ARG85 |
| A | GLU197 |
| A | PG4612 |
| A | HOH709 |
| A | HOH851 |
| site_id | AE5 |
| Number of Residues | 10 |
| Details | binding site for residue MES A 623 |
| Chain | Residue |
| A | LEU195 |
| A | PRO238 |
| A | THR239 |
| A | THR339 |
| A | GLY340 |
| A | ASN341 |
| A | FAD601 |
| A | GOL608 |
| A | HOH723 |
| A | HOH860 |
| site_id | AE6 |
| Number of Residues | 7 |
| Details | binding site for residue MES A 624 |
| Chain | Residue |
| A | LYS41 |
| A | MET43 |
| A | LYS257 |
| A | PHE258 |
| A | LEU259 |
| A | PRO260 |
| A | ASN435 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue SMA A 625 |
| Chain | Residue |
| A | TYR476 |
| A | ARG479 |
| A | P6G607 |
| A | HOH754 |
| site_id | AE8 |
| Number of Residues | 14 |
| Details | binding site for residue SMA A 626 |
| Chain | Residue |
| A | TRP63 |
| A | PRO92 |
| A | ALA393 |
| A | GLN394 |
| A | HIS397 |
| A | LEU444 |
| A | ILE459 |
| A | SER461 |
| A | TYR482 |
| A | SER484 |
| A | MET485 |
| A | FAD601 |
| A | GOL608 |
| A | PGE616 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 66 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
