SMTL ID : 7orb.2 (1 other biounit)

Crystal structure of the L452R mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-75 and COVOX-253 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.1: 4 residues within 4Å: Chain A: F.15, G.16, F.19, N.20 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.2: 4 residues within 4Å: Chain B: H.100, N.102, S.105, Y.107 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: F.19, N.20, S.50, F.51, W.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.50 GOL.4: 2 residues within 4Å: Chain A: N.31, R.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.32 GOL.7: 5 residues within 4Å: Chain B: G.8, P.9, G.116, T.117, M.118 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.8, B:M.118 GOL.10: 11 residues within 4Å: Chain B: F.176, P.177, V.179, S.187, L.188, S.189 Chain C: Q.161, S.163, S.177, S.178, T.179 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.163, C:T.179, B:S.189, B:S.189 GOL.11: 10 residues within 4Å: Chain D: F.180, P.181, V.183, S.191, L.192, S.193 Chain E: S.162, S.176, S.177, T.178 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:F.180, D:V.183, D:S.193, D:S.193, E:S.176 Water bridges: D:S.191, E:T.178 GOL.13: 4 residues within 4Å: Chain D: D.54, G.55, S.71, R.72 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.72, D:N.74 GOL.19: 3 residues within 4Å: Chain E: Y.49, A.50, S.53 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.53, E:S.53 Water bridges: E:S.31

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: R.23, F.24, A.25, S.26, N.127, Y.128 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Water bridges: A:S.26, E:S.30, E:S.30 PEG.6: 6 residues within 4Å: Chain A: S.154, T.155, P.156 Chain C: S.32, Y.50, G.51 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.32 PEG.12: 4 residues within 4Å: Chain D: V.2, R.98, D.115 Chain E: Q.55 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.98, D:D.115, E:Q.55

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

CL.8: 6 residues within 4Å: Chain B: R.44, L.45, E.46, W.47 Chain C: T.98, F.99 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain D: H.178 Chain E: D.167 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain D: T.165, V.166 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 5 residues within 4Å: Chain A: V.160, E.161, G.162 Chain C: Y.33, G.93 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.93, A:V.160, A:F.163

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.14: 9 residues within 4Å: Chain D: Y.159, E.162, P.163, V.164, T.179, F.180, P.181, A.182, L.192 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.162, D:E.162, D:V.164, D:F.180, D:A.182 Water bridges: D:E.162 Salt bridges: D:E.162

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 6 residues within 4Å: Chain A: Q.175 Chain D: S.52, Q.53, N.57, Y.110, Y.111 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.53, D:N.57, D:Y.111, A:Q.175 Water bridges: D:Y.111 PO4.16: 5 residues within 4Å: Chain B: G.56, T.58 Chain D: A.106, R.107, N.108 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:A.106, D:N.108, D:N.108, B:T.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell (2021)

Release Date

2021-07-07

Peptides

Spike protein S1: A
COVOX-253 Fab heavy chain: B
COVOX-253 Fab light chain: C
COVOX-75 Fab heavy chain: D
COVOX-75 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
C

C
D

D
E

E
F

Spike protein S1

COVOX-253 Fab heavy chain

COVOX-253 Fab light chain

COVOX-75 Fab heavy chain

COVOX-75 Fab light chain

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