X-ray Structures - HIV
Substrate Complexes of HIV-1 Protease
| Inactive Protease Variant | Substrate | Resolution (Å) | R-factor (%) | Rfree | PDB code |
|---|---|---|---|---|---|
| Wild-type (HIV-1 B) | MA-CA | 2.90 | 19.7 | 24.8 | 1KJ4 |
| " | CA-p2 | 2.00 | 19.7 | 23.3 | 1F7A |
| " | p2-NC | 2.00 | 20.6 | 24.9 | 1KJ7 |
| " | NC-p1 | 2.10 | 20.6 | 23.3 | 1TSU |
| " | p1-p6 | 2.00 | 20.3 | 25.1 | 1KJF |
| " | RT-RH | 2.00 | 18.4 | 22.6 | 1KJG |
| " | RH-IN | 2.00 | 18.8 | 22.7 | 1KJH |
| " | NC-p1_C | 1.85 | 19.5 | 24.3 | - |
| " | TF-PR | 2.30 | 17.0 | 22.5 | - |
| V82A | MA-CA | 1.90 | 20.1 | 22.7 | 1MT7 |
| " | CA-p2 | 2.15 | 20.8 | 24.3 | 1MT8 |
| " | p1-p6 | 2.00 | 17.9 | 21.0 | 1MT9 |
| " | NC-p1AP2V | 2.00 | 19.5 | 23.1 | 1TSQ |
| " | TF(NC*)-p6pol | 1.43 | 18.6 | 22.7 | - |
| T80V | p1-p6 | 2.20 | 19.6 | 24.7 | - |
| V82T/I84V/L63P | CA-p2 | 1.80 | 19.6 | 24.3 | - |
| Wild-type (flap intermediate) | NC-p1 | 1.85 | 19.4 | 24.3 | 2FNS |
| V82A (flap intermediate) | NC-p1AP2V | 1.44 | 18.7 | 21.4 | 2FNT |
| Wild-type | p6pol-PR | 2.30 | 19.4 | 23.7 | - |
| " | RT-RHEP3D/VP2'L | 2.00 | 19.5 | 25.7 | 2NXD |
| " | RT-RHTP2V | 2.00 | 16.0 | 21.6 | 2NXL |
| " | RT-RHEP3Q | 2.25 | 18.7 | 24.3 | 2NXM |
| CRF01_AE wild-type | p1-p6 | 2.80 | 20.3 | 25.8 | 3D3T |
| HIV-1 B wild-type | p1-p6L449F | 1.85 | 16.3 | 21.3 | - |
| " | p1-p6S451N | 1.75 | 14.1 | 17.5 | - |
| " | p1-p6L449F/S451N | 1.65 | 17.3 | 20.5 | - |
| D30N/N88D | p1-p6 | 1.78 | 20.0 | 25.5 | - |
| " | p1-p6S451N | 1.75 | 18.0 | 22.9 | - |
| " | p1-p6L449F/S451N | 1.90 | 20.0 | 24.4 | - |
| C67L/C95M (Wild-type tethered dimer) | RT-RH | 1.90 | 21.3 | 25.2 | - |
| " | p2-NC | 1.66 | 23.1 | 26.2 | - |
| " | CA-p2 | 1.90 | 24.1 | 27.3 | - |
| D30F/A28S/G48R (Tethered dimer) | RT-RH | 1.90 | 20.3 | 26.0 | - |
| " | p2-NC | 1.70 | 20.3 | 24.7 | - |
| Active Protease Variant | Substrate | Resolution (Å) | R-factor (%) | Rfree | PDB code |
| Q7K/L33I/L63P | RH-INRKIL | 1.70 | 16.9 | 19.3 | - |
| " | MA-CASQNY | 2.20 | 16.5 | 20.7 | - |
| " | CA-p2RVL*LVAA | 1.90 | 16.7 | 22.3 | - |
| " | p1-p6GNF*LQ | 1.85 | 16.7 | 19.6 | - |
| " | RT-RHAETF*YVD | 2.00 | 18.4 | 20.5 | - |
Inhibitor Complexes of HIV-1 Protease
| Protease Variant | Inhibitor | Resolution (Å) | R-factor (%) | Rfree | PDB code |
|---|---|---|---|---|---|
| Wild-type | APV | 1.75 | 19.0 | 22.6 | 3EKV |
| " | ATV | 1.70 | 17.3 | 20.5 | 3EKY |
| " | DRV | 1.20 | 13.9 | 17.9 | 1T3R |
| " | IDV | 2.00 | 18.5 | 21.8 | - |
| " | LPV | 1.95 | 19.2 | 23.6 | 2Q5K |
| " | NFV | 1.97 | 18.4 | 23.0 | 3EKX |
| " | Roche | 1.60 | 16.3 | 19.8 | 2F3K |
| L63P/V82T/I84V | APV | 2.20 | 20.3 | 24.4 | 1T7J |
| " | ATV | 1.60 | 19.2 | 21.7 | 3EL9 |
| " | DRV | 1.35 | 16.3 | 20.0 | 1T7I |
| " | IDV | 2.20 | 19.4 | 23.1 | 1K6C |
| " | NFV | 1.60 | 19.8 | 22.5 | 3EL5 |
| " | SQV | 2.00 | 19.0 | 22.3 | 3EL4 |
| L10I/G48V/I54V/L63P/V82A | APV | 2.15 | 19.6 | 25.5 | 3EKP |
| " | ATV | 1.60 | 18.7 | 22.2 | 3EKW |
| " | DRV | 1.97 | 20.9 | 25.6 | 3EKT |
| " | NFV | 1.60 | 18.2 | 21.2 | 3EL0 |
| " | SQV | 2.20 | 19.5 | 24.6 | 3EKQ |
| I50L/A71V | APV | 2.20 | 18.5 | 24.7 | 3EM3 |
| " | ATV | 2.10 | 18.0 | 24.8 | 3EM4 |
| " | DRV | 2.10 | 18.6 | 24.0 | 3EM6 |
| T80N | SQV | 1.50 | 17.1 | 19.7 | 2FGV |
| T80S | SQV | 2.00 | 17.6 | 23.2 | 2FGU |
| CRF01_AE (Q7K) | DRV | 1.96 | 20.0 | 25.9 | 3LZS |
| CRF01_AE (Q7K/N88S) | DRV | 1.76 | 19.6 | 23.9 | 3LZU |
| Wild-type | CARB2-KB45 | 1.80 | 16.5 | 20.8 | 2PSV |
| " | MIT1-AC87 | 1.85 | 16.6 | 20.5 | 2QHZ |
| " | MIT1-KK81 | 2.00 | 15.6 | 20.5 | 2QI1 |
| " | MIT1-KK80 | 2.10 | 17.0 | 23.0 | 2QI0 |
| " | MIT1-AC86 | 1.85 | 15.9 | 19.7 | 2QHY |
| " | CARB2-AD37 | 1.95 | 16.1 | 19.8 | 2PSU |
| " | MIT2-AD94 | 1.95 | 17.4 | 21.0 | 2QI3 |
| " | MIT2-AD86 | 1.85 | 17.4 | 20.3 | 2QI7 |
| " | MIT2-AD93 | 1.80 | 17.3 | 20.3 | 2QI4 |
| " | MIT2-KB98 | 1.85 | 17.0 | 21.2 | 2QI6 |
| " | UMass1-KB60 | 1.85 | 16.9 | 22.1 | 3GI4 |
| " | MIT2-KC08 | 1.85 | 17.3 | 21.0 | 2QI5 |
| " | UMass1-KB62 | 1.80 | 17.0 | 19.4 | 3GI5 |
| " | UMass1-AD78 | 1.85 | 16.4 | 19.6 | 3GI6 |
| " | UMass1-KB19 | 1.80 | 16.0 | 18.5 | 2I0A |
| " | UMass1-AD81 | 1.95 | 16.6 | 21.6 | 2I0D |
| " | UMass2I-KK44 | 1.90 | 17.5 | 23.5 | 2Q55 |
| " | UMass2I-KB73 | 1.85 | 17.4 | 22.4 | 2Q54 |
| " | KC47 | 1.90 | 17.2 | 21.6 | - |
| " | KC53 | 1.95 | 16.5 | 20.1 | 3MXD |
| " | KC32 | 1.85 | 18.0 | 22.3 | 3MXE |
| " | KD14 | 1.90 | 17.9 | 21.6 | 3O9A |
| " | KD20 | 1.85 | 17.5 | 22.4 | 3O9C |
| " | KD26 | 1.70 | 16.6 | 22.8 | 3O9H |
| " | KD13 | 1.95 | 17.7 | 22.4 | 3O99 |
| " | AF60 | 1.50 | 16.7 | 19.7 | 3O9E |
| " | AF61 | 1.45 | 17.2 | 19.5 | 3O9I |
| " | AF57 | 1.75 | 17.3 | 20.3 | - |
| " | AF53 | 1.65 | 17.6 | 20.3 | 3O9G |
| " | KD25 | 1.50 | 16.5 | 18.9 | 3O9B |
| " | KD27 | 1.70 | 16.9 | 20.3 | 3O9F |
| " | KD19 | 1.85 | 17.4 | 22.6 | 3O9D |
| " | AF71 | 1.75 | 17.0 | 19.4 | 3SA6 |
| " | AF72 | 1.80 | 17.6 | 21.3 | 3SA4 |
| " | AF55 | 1.80 | 17.6 | 21.3 | 3SA7 |
| " | AG23 | 1.65 | 17.2 | 20.3 | 3SA3 |
| " | AF80 | 1.50 | 18.1 | 20.4 | 3SAC |
| " | KB83 | 1.50 | 16.4 | 19.3 | 3SA8 |
| " | AF69 | 1.65 | 17.5 | 20.3 | 3SA5 |
| " | AF68 | 1.70 | 17.4 | 21.4 | 3SA9 |
| " | AF77 | 1.95 | 17.3 | 22.8 | 3SAA |
| " | AF78 | 1.50 | 19.4 | 22.2 | 3SAB |
| " | MKP73 | 1.40 | 17.3 | 18.9 | - |
| " | MKP86 | 1.40 | 17.9 | 20.4 | - |
| " | MKP97 | 1.55 | 17.0 | 19.6 | - |
| " | MKP56 | 1.78 | 16.0 | 21.7 | - |
| " | TMC114-A1 | 2.00 | 15.5 | 20.3 | - |
| " | TMC114-A2 | 1.83 | 18.1 | 22.8 | - |
| " | TMC114-A3 | 2.00 | 18.2 | 23.8 | - |
| " | t745182 | 1.90 | 17.9 | 22.7 | 3R4B |
| " | t746406 | 1.90 | 17.8 | 21.8 | - |
| " | t746826 | 1.95 | 16.9 | 21.0 | - |
| " | p867883 | 2.00 | 18.7 | 23.2 | 2Q3K |
| " | p386395 (ATV) | 1.80 | 17.6 | 20.9 | - |
| " | t546744 | 2.05 | 18.3 | 22.9 | - |