Table 2. R.m.s.d. values (Å) for core Cα superpositions of molecule A of M-PMV PR on molecule B and on protomers of aspartic retroviral proteases, N- and C-terminal domains of porcine pepsin and the retropepsin-like putative protease domain of the eukaryotic protein Ddi1 (PDB codes are given in parentheses).
R.m.s.d. values for core Cα atoms are shown in the first row and were calculated using the SSM server (Krissinel & Henrick, 2004 ▶). Values in the second row are for all common Cα atoms (calculated in ALIGN; Cohen, 1997 ▶). The coordinates of the NMR model 1nso were energy-minimized in vacuo and in water. The following abbreviations are used to identify different retroviral proteases: M-PMV, Mason–Pfizer monkey virus; HIV-1, human immunodeficiency virus type 1; SIV, simian immunodeficiency virus; ASV, avian sarcoma virus; FIV, feline immunodeficiency virus; EIAV, equine infectious anaemia virus; HTLV-1, human T-cell leukaemia virus type 1; XMRV, xenotropic murine leukaemia virus-related virus.
| M-PMV | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NMR (1nso) | Pepsin (4pep) | |||||||||||||
| B | Foldit | Vacuo | Water | HIV-1 (3hvp)† | HIV-1 (4hvp)‡ | SIV (1yth)‡ | ASV (2rsp)†§ | FIV (4fiv)‡ | EIAV (2fmb)‡ | HTLV-1 (3liy)‡ | XMRV (3nr6)† | Ddi1 (2i1a) | N | C |
| 0.18 | 2.08 | 3.04 | 2.57 | 2.14 | 2.17 | 2.09 | 1.54 | 1.94 | 1.65 | 2.05 | 1.95 | 2.23 | 4.17 | 3.13 |
| 0.18 | 2.87 | 5.51 | 4.33 | 8.92 | 9.06 | 7.73 | 7.95 | 4.28 | 8.23 | 3.50 | 10.49 | 9.77 | 4.44 | 5.93 |
†
Apo form.
‡
Inhibitor complex.
§
Flap loops missing.