Table 2.
GAPDH complexes with substrate or substrate analogue.
| PDB number | Reference | NAD present | Substrate | No. of subunits with substrate | Ps or New Pi* site | Soaked or Co-crystallized |
| CpGAPDH | This structure | Yes | D-glyceraldehyde 3-phosphate | 4 | New Pi& | Co-crystal |
| 1GYP | 17 | Yes | PO4 | 4 | Ps and new Pi | Co-crystal |
| 1DC4 | 16 | No | D-glyceraldehyde 3-phosphate | 2# | New Pi | Soaked |
| 1NQO | 15 | Yes | D-glyceraldehyde 3-phosphate | 4 | Ps | Soaked |
| 3CMC | 12 | Yes | D-glyceraldehyde 3-phosphate | 4 | New Pi | Soaked |
| 1ML3 | 14 | Yes | (3-formyl-but-3-enyl)-phosphonic acid | 3+ | Ps | Co-crystal |
| 1QXS | 18 | Yes | 1,3-biphospho-D-glyceric acid | 1$ | Ps | Co-crystal |
* The 'new Pi' site is defined as the site of the phosphate in 1GYP, which contains only phosphate and NAD.
&Only subunits A, B and C. The D-G3H molecule in subunit D occupies a different position that does not correspond to any previously reported phosphate position.
# Two subunits per asymmetric unit.
+ Two conformers in the structure. Subunit D has only conformer A, and its phosphate moiety binds in the 'Ps' site. Subunits B and C have both conformers at 50% occupancy; the phosphate moiety in conformer B binds in a site that is 2.5 to 2.8 Å from the 'new Pi' site.
$ Only one subunit (subunit C) binds the analogue. One of the phosphate moieties binds in the 'Ps' site. The other binds in a site that is 2.8 Å from the 'new Pi' site.