SMTL ID : 7orb.1 (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- MAN- FUC: alpha-D-mannopyranose-(1-3)-[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-MAN-FUC.1: 5 residues within 4Å: Chain A: F.15, G.16, N.20, S.50 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.50

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

NAG-NAG-FUC.2: 5 residues within 4Å: Chain B: H.100, N.102, S.105, C.106, Y.107 No protein-ligand interaction detected (PLIP)

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.19, N.20, S.50, F.51, W.113 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.19, A:S.50 GOL.5: 3 residues within 4Å: Chain A: R.80 Chain B: T.30, M.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.80 GOL.6: 4 residues within 4Å: Chain B: K.153, D.154, S.183 Chain C: T.181 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.154, B:S.183 GOL.7: 2 residues within 4Å: Chain B: Q.115 Chain C: G.42 No protein-ligand interaction detected (PLIP) GOL.10: 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.11: 7 residues within 4Å: Chain A: Q.175 Chain D: P.33, S.52, Q.53, N.57, Y.110, Y.111 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:Q.175, D:Q.53, D:Q.53, D:N.57 GOL.12: 9 residues within 4Å: Chain D: F.180, P.181, V.183, S.191, L.192, S.193 Chain E: S.162, S.176, T.178 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:S.162, E:S.176, D:F.180, D:V.183, D:S.193, D:S.193 GOL.14: 3 residues within 4Å: Chain A: Y.126 Chain E: A.50, S.53 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.53 GOL.15: 7 residues within 4Å: Chain D: V.177, H.178 Chain E: T.164, E.165, Q.166, D.167, S.168 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:V.177, D:H.178, E:S.168 Water bridges: D:T.179

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

PEG.4: 7 residues within 4Å: Chain A: S.52, T.53, G.81, D.82, V.84, G.181, Y.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.53, A:T.53, A:D.82

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

CL.8: 4 residues within 4Å: Chain B: R.44, W.47 Chain C: T.98, F.99 Ligand excluded by PLIP

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

TRS.9: 7 residues within 4Å: Chain A: V.160, E.161, G.162, F.163, C.165 Chain C: Y.33, G.93 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.33, A:V.160, A:F.163

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

PO4.13: 6 residues within 4Å: Chain B: G.56, N.57, T.58 Chain D: A.106, R.107, N.108 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:N.108, B:T.58, B:T.58 Water bridges: B:Y.60

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
R

B
H

C
L

D
A

E
B

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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