Receptor binding domain (RBD) structures based on PDB ID: 6M0J
D614G mutation
PDB ID: 7BNN (RBD)
PDB ID: 6M0J (ACE2)
Mink cluster 5 variant
PDB ID: 7LWM (RBD)
PDB ID: 6M0J (ACE2)
D614G mutation spike RBD in complex with human angiotensin converting-enzyme 2 (hACE2) (6M0J)
Code: 6M0J-7BNN
Mink cluster 5 variant spike RBD, in complex with hACE2 (6M0J)
Code: 6M0J-7LWM
Details
D614G mutation spike RBD in complex with hACE2 (6M0J, Gromacs 2021.2, force field: CHARMM36):
6M0J-7BNN: D614G mutation spike RBD (7BNN), in complex with hACE2 (6M0J) (100 ns, 774095 atoms)
Mink cluster 5 variant spike RBD, in complex with hACE2 (6M0J, Gromacs 2021.2, force field: CHARMM36):Â
6M0J-7LWM: Mink cluster 5 variant spike RBD (7LWM), in complex with hACE2 (6M0J) (100 ns, 746031 atoms)
Alpha B.1.1.7 variant
PDB ID: 7MJN (RBD)
PDB ID: 6M0J (ACE2)
PDB ID: 6M0J (manually mutated RBD)
Alpha B.1.1.7 variant spike RBD, in complex with hACE2 (6M0J)
Code: 6M0J-7MJN
Alpha B.1.1.7 variant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-ALPHA
Details
Alpha B.1.1.7 variant spike RBD, in complex with hACE2 (6M0J, Gromacs 2021.2, force field: CHARMM36):Â
6M0J-7MJN: Alpha B.1.1.7 variant spike RBD, in complex with hACE2 (6M0J) (100 ns, 735274 atoms)
Alpha B.1.1.7 variant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):Â
6M0J-ALPHA-1: Alpha B.1.1.7 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713168 atoms)
6M0J-ALPHA-2: Alpha B.1.1.7 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713168 atoms)
6M0J-ALPHA-3: Alpha B.1.1.7 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713168 atoms)
6M0J-ALPHA-4: Alpha B.1.1.7 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713168 atoms)
G485R mutation
PDB ID: 7LO4 (RBD)
PDB ID: 6M0J (ACE2)
PDB ID: 6M0J (manually mutated)
G485R mutation spike RBD, in complex with hACE2 (6M0J)
Code: 6M0J-7LO4
G485R mutation spike RBD ('manual'), in complex with hACE2
Code: 6M0J-G485R
Details
G485R mutation spike RBD, in complex with hACE2 (6M0J, Gromacs 2021.2, force field: CHARMM36):Â
6M0J-7LO4: G485R mutation spike RBD, in complex with hACE2 (6M0J) (100 ns, 705245 atoms)
G485R mutation spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):Â
6M0J-G485R: G485R mutation spike RBD ('manual'), in complex with hACE2 (100 ns, 713156 atoms)
Beta B.1.351 variant
PDB ID: 7LYN (RBD)
PDB ID: 6M0J (ACE2)
Beta B.1.351 variant spike RBD, in complex with hACE2 (6M0J)
Code: 6M0J-7LYN
Details
Beta B.1.351 variant spike RBD, in complex with hACE2 (6M0J, Gromacs 2021.2, force field: CHARMM36):Â
6M0J-7LYN: Beta B.1.351 variant spike RBD (7LYN), in complex with hACE2 (6M0J) (100 ns, 758374 atoms)
Gamma P.1 variant
PDB ID: 7NXC (RBD)
PDB ID: 6M0J (ACE2)
PDB ID: 6M0J (manually mutated)
Gamma P.1 variant spike RBD, in complex with hACE2 (6M0J)
Code: 6M0J-7NXC
Gamma P.1 variant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-GAMMA
Details
Gamma P.1 variant spike RBD, in complex with hACE2 (6M0J, Gromacs 2021.2, force field: CHARMM36):Â
6M0J-7NXC: Gamma P1 variant spike RBD, in complex with hACE2 (6M0J) (100 ns, 698243 atoms)
Gamma P.1 variant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):
6M0J-GAMMA-1: Gamma P1 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713181 atoms)
6M0J-GAMMA-2: Gamma P1 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713181 atoms)
6M0J-GAMMA-3: Gamma P1 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713181 atoms)
Epsilon B.1.429 variant
PDB ID: 6M0J (manually mutated)
Kappa B.1.617.1 variant
PDB ID: 6M0J (manually mutated)
Mu B.1.621 variant
PDB ID: 6M0J (manually mutated)
Epsilon B.1.429 variant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-EPSI
Kappa B.1.617.1 variant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-KAPPA
Mu variant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-MU
Details
Epsilon B.1.429 variant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):Â
6M0J-EPSI-1: Epsilon B.1.429 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713159 atoms)
6M0J-EPSI-2: Epsilon B.1.429 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713159 atoms)
6M0J-EPSI-3: Epsilon B.1.429 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713159 atoms)
Kappa B.1.617.1 variant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):
6M0J-KAPPA-1: Kappa B.1.617.1 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713157 atoms)
6M0J-KAPPA-2: Kappa B.1.617.1 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713157 atoms)
6M0J-KAPPA-3: Kappa B.1.617.1 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713157 atoms)
Mu variant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):
6M0J-MU-1: Mu variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713174 atoms)
6M0J-MU-2: Mu variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713174 atoms)
6M0J-MU-3: Mu variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713174 atoms)
Delta B.1.617.1 variant
PDB ID: 6M0J (manually mutated)
PDB ID: 6M0J (manually mutated)
PDB ID: 6M0J (manually mutated)
Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-DELTA
Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-DELTA
Delta plus variant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-DPLUS
Details
Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):
6M0J-DELTA-1: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713148 atoms)
6M0J-DELTA-2: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713148 atoms)
6M0J-DELTA-3: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713148 atoms)
6M0J-DELTA-4: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713148 atoms)
6M0J-DELTA-5: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713148 atoms)
6M0J-DELTA-6: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713148 atoms)
Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):Â
6M0J-DELTA-7: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181172 atoms)
6M0J-DELTA-8: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181172 atoms)
6M0J-DELTA-9: Delta B.1.617.2 variant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181172 atoms)
Delta plus variant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):
6M0J-DPLUS: Delta plus variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713159 atoms)
Omicron B.1.1.529 variant
PDB ID: 6M0J (manually mutated)
Omicron B.1.1.529 variant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-OMI
Omicron BA.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-OMI
Omicron BA.2 subvariant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-BA2
Details
Omicron B.1.1.529 variant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):
6M0J-OMI-1: Omicron B.1.1.529 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713196 atoms)
6M0J-OMI-2: Omicron B.1.1.529 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713196 atoms)
6M0J-OMI-3: Omicron B.1.1.529 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713196 atoms)
6M0J-OMI-4 Omicron B.1.1.529 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713196 atoms)
6M0J-OMI-5: Omicron B.1.1.529 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713196 atoms)
6M0J-OMI-6: Omicron B.1.1.529 variant spike RBD ('manual'), in complex with hACE2 (100 ns, 713196 atoms)
Omicron BA.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):
6M0J-OMI-7: Omicron BA.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181247 atoms)
6M0J-OMI-8: Omicron BA.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181247 atoms)
6M0J-OMI-9: Omicron BA.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181247 atoms)
Omicron BA.2 subvariant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36):
6M0J-BA2-1: Omicron BA.2 subvariant spike RBD ('manual'), in complex with hACE2 (100 ns, 713174 atoms)
6M0J-BA2-2: Omicron BA.2 subvariant spike RBD ('manual'), in complex with hACE2 (100 ns, 713174 atoms)
6M0J-BA2-3: Omicron BA.2 subvariant spike RBD ('manual'), in complex with hACE2 (100 ns, 713174 atoms)
Omicron BA.3 subvariant spike RBD ('manual'), in complex with hACE2
Code: 6M0J-BA3
Omicron BA.4/BA.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-BA4BA5
Omicron BA.2.12.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-BA2121
Details
Omicron BA.3 subvariant spike RBD ('manual'), in complex with hACE2 (Gromacs 2021.2, force field: CHARMM36)
6M0J-BA3-1: Omicron BA.3 subvariant spike RBD ('manual'), in complex with hACE2 (100 ns, 713194 atoms)
6M0J-BA3-2: Omicron BA.3 subvariant spike RBD ('manual'), in complex with hACE2 (100 ns, 713194 atoms)
6M0J-BA3-3: Omicron BA.3 subvariant spike RBD ('manual'), in complex with hACE2 (100 ns, 713194 atoms)
Omicron BA.4/BA.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):
6M0J-BA4BA5-1: Omicron BA.4/BA.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181210 atoms)
6M0J-BA4BA5-2: Omicron BA.4/BA.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181210 atoms)
6M0J-BA4BA5-3: Omicron BA.4/BA.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181210 atoms)
Omicron BA.2.12.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):
6M0J-BA2121-1: Omicron BA.2.12.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181202 atoms)
6M0J-BA2121-2: Omicron BA.2.12.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181202 atoms)
6M0J-BA2121-3: Omicron BA.2.12.1 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181202 atoms)
Omicron BA.2.75 subvariant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-BA275
Omicron BA.4.6 subvariant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-BA46
Omicron BA.5.9 subvariant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-BA59
Details
Omicron BA.2.75 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):
6M0J-BA275-1: Omicron BA.2.75 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181231 atoms)
6M0J-BA275-2: Omicron BA.2.75 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181231 atoms)
6M0J-BA275-3: Omicron BA.2.75 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181231 atoms)
Omicron BA.4.6 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):
6M0J-BA46-1: Omicron BA.4.6 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181192 atoms)
6M0J-BA46-2: Omicron BA.4.6 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181192 atoms)
6M0J-BA46-3: Omicron BA.4.6 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181192 atoms)
Omicron BA.5.9 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):
6M0J-BA59-1: Omicron BA.5.9 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181203 atoms)
6M0J-BA59-2: Omicron BA.5.9 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181203 atoms)
6M0J-BA59-3: Omicron BA.5.9 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181203 atoms)
Omicron XBB.1.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-XBB15
Omicron XBB.1.16 subvariant spike RBD ('manual'), in complex with hACE2 (ZN)
Code: 6M0J-XBB116
Details
Omicron XBB.1.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):
6M0J-XBB15-1: Omicron XBB.1.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181178 atoms)
6M0J-XBB15-2: Omicron XBB.1.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181178 atoms)
6M0J-XBB15-3: Omicron XBB.1.5 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181178 atoms)
Omicron XBB.1.16 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (Gromacs 2018.4, force field: CHARMM36):
6M0J-XBB116-1: Omicron XBB.1.16 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181195 atoms)
6M0J-XBB116-2: Omicron XBB.1.16 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181195 atoms)
6M0J-XBB116-3: Omicron XBB.1.16 subvariant spike RBD ('manual'), in complex with hACE2 (ZN) (200 ns, 181195 atoms)
BNT162b1 Vaccine
PDB ID: 7L7F (RBD)
PDB ID: 6M0J (ACE2)
BNT162b1 Vaccine spike RBD, in complex with hACE2Â
Details
BNT162b1 Vaccine spike RBD (7L7F), in complex with hACE2 (6M0J, Gromacs 2021.2, force field: CHARMM36)
6M0J-7L7F: BNT162b1 Vaccine spike RBD (7L7F), in complex with hACE2 (6M0J) (100 ns, 697425 atoms)