SMTL ID : 8df5.1

SARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S309 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: Y.100 Chain B: Y.50 Chain K: F.43, G.44, F.47, N.48, V.72 Ligands: EDO.64 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain C: Y.100 Chain D: Y.50 Chain L: F.43, G.44, F.47, N.48, V.72 No protein-ligand interaction detected (PLIP)

30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: Y.159, E.162, P.163, V.164, P.181, A.182 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: L.155, V.183, S.191, L.192, S.193 Chain B: T.178 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: Q.38, R.46, I.59, P.60, F.63 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain B: L.11, L.13, R.18, A.19, T.20 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain B: A.144, K.145, V.146, E.161 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: P.141, E.143, Q.199 Ligands: EDO.12 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: S.12, E.105, E.143 Ligands: EDO.11 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: P.119, Y.186, N.210, R.211, G.212, E.213 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain C: Y.159, E.162, P.163, V.164, P.181, A.182 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain D: A.144, K.145, V.146, E.161 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain D: T.10, S.12, P.141, E.143 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain E: G.319, L.320, P.321, Q.552, F.555 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain E: H.34, E.37 Chain K: R.108 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain E: G.214, Y.215, D.216, Y.217, T.567, K.577 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain E: D.225, H.228, N.578, M.579 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain F: G.319, Q.552, F.555 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain F: Y.215, D.216, Y.217, K.577 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain F: D.225, H.228, N.578, M.579 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain F: H.34, E.37 Chain L: R.108 Ligand excluded by PLIP EDO.54: 7 residues within 4Å: Chain H: Q.37, K.39, K.45, R.61, F.62, E.81, D.82 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain H: Q.6, P.101 Chain J: A.14, D.17 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain H: A.14, D.17 Chain J: Q.6, S.9, P.101 Ligand excluded by PLIP EDO.59: 6 residues within 4Å: Chain I: Y.59 Chain J: P.95 Chain L: S.80, T.81, F.82, K.83 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain I: D.99, Y.106, D.108, Y.109 Chain J: Q.55 Ligand excluded by PLIP EDO.61: 7 residues within 4Å: Chain J: Q.37, K.39, K.45, R.61, F.62, E.81, D.82 Ligand excluded by PLIP EDO.62: 8 residues within 4Å: Chain I: L.148, S.184, L.185, S.186 Chain J: Q.161, S.177, S.178, T.179 Ligand excluded by PLIP EDO.64: 5 residues within 4Å: Chain K: V.72, S.76, F.79 Ligands: NAG-NAG.1, EDO.65 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain K: F.47, N.48, S.78, F.79, W.141 Ligands: EDO.64 Ligand excluded by PLIP EDO.66: 8 residues within 4Å: Chain K: P.131, D.133, F.134, T.135, F.169, S.219, F.220, E.221 Ligand excluded by PLIP EDO.68: 6 residues within 4Å: Chain F: H.34, E.35, D.38 Chain L: Y.154, Q.198, S.199 Ligand excluded by PLIP

22 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Chain A: N.169 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: T.72, D.73, T.74 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: E.46, W.47 Chain B: T.97, F.98 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: N.59, R.102 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: E.108, S.109 Chain L: R.51 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain D: Q.38, R.46 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain C: E.46, W.47 Chain D: T.97, F.98 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain E: R.169, W.477, W.478, K.481, D.499 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain E: R.518, T.519 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain E: F.40, D.350, G.352, R.393 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain E: Y.515, R.518 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain E: E.375 Ligands: ZN.21 Ligand excluded by PLIP CL.48: 4 residues within 4Å: Chain F: R.169, W.477, W.478, D.499 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain F: D.350, R.393 Ligand excluded by PLIP CL.50: 2 residues within 4Å: Chain F: W.271, R.273 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain F: E.375, E.402 Ligands: ZN.37 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain F: E.232, N.580, R.582 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain G: T.40, T.41 Ligand excluded by PLIP CL.57: 1 residues within 4Å: Chain H: S.157 Ligand excluded by PLIP CL.58: 1 residues within 4Å: Chain H: S.28 Ligand excluded by PLIP CL.67: 4 residues within 4Å: Chain E: H.34 Chain K: R.108, E.111, N.122 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain L: R.60, F.169 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.21: 5 residues within 4Å: Chain E: H.374, E.375, H.378, E.402 Ligands: CL.36 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.374, E:H.378, E:E.402 ZN.37: 5 residues within 4Å: Chain F: H.374, E.375, H.378, E.402 Ligands: CL.51 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.374, F:H.378, F:E.402

13 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.22: 5 residues within 4Å: Chain E: N.53, T.55, E.57, N.58, Q.340 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:N.53, E:T.55, E:E.57, E:N.58, E:Q.340 NAG.23: 3 residues within 4Å: Chain E: K.26, N.90, V.93 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.26, E:N.90 NAG.24: 1 residues within 4Å: Chain E: N.322 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.322 Water bridges: E:N.322 NAG.25: 4 residues within 4Å: Chain E: Q.81, Q.101, Q.102, N.103 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.101 NAG.26: 2 residues within 4Å: Chain E: S.420, N.546 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.420, E:S.420, E:S.420, E:N.546 NAG.27: 1 residues within 4Å: Chain E: N.432 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.432 NAG.38: 5 residues within 4Å: Chain F: N.53, T.55, E.57, N.58, Q.340 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.53, F:T.55, F:E.57, F:N.58 NAG.39: 3 residues within 4Å: Chain F: K.26, N.90, V.93 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.26, F:N.90 NAG.40: 4 residues within 4Å: Chain F: S.420, D.543, S.545, N.546 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:S.420 Hydrogen bonds: F:S.420, F:N.546 NAG.41: 1 residues within 4Å: Chain F: N.322 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.322 NAG.42: 5 residues within 4Å: Chain F: Q.81, Q.101, Q.102, N.103, N.194 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.101, F:Q.101, F:N.103 Water bridges: F:G.104 NAG.43: 1 residues within 4Å: Chain F: N.432 No protein-ligand interaction detected (PLIP) NAG.63: 2 residues within 4Å: Chain K: N.36, T.38 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.36, K:T.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Starr, T.N. et al., Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution. Science (2022)

Release Date

2022-08-03

Peptides

S309 Fab Heavy Chain: AC
S309 Fab Light Chain: BD
Angiotensin-converting enzyme 2: EF
S304 Fab Heavy Chain: GI
S304 Fab Light Chain: HJ
Spike protein S1: KL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

G
H

I
M

H
L

J
N

K
R

L
S

S309 Fab Heavy Chain

S309 Fab Light Chain

Angiotensin-converting enzyme 2

S304 Fab Heavy Chain

S304 Fab Light Chain

Spike protein S1

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