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):

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):

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):

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):

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):

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):

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):

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):

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)

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):

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 hACE2

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)

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