SMTL ID : 7nx8.1

Crystal structure of the K417T mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

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

Ligands

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

NAG.1: 2 residues within 4Å: Chain C: G.16, N.20 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain C: T.53, G.81, D.82, V.84, V.180, G.181, Y.185 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.53, C:T.53, C:D.82, C:V.180 Water bridges: C:S.52 GOL.6: 8 residues within 4Å: Chain C: R.80, T.94, Y.130, L.132 Chain D: E.99, S.101, N.104 Chain E: Y.92 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:E.99, D:S.101, D:N.104, C:R.80, C:T.94, C:T.94 Water bridges: C:I.95 GOL.10: 5 residues within 4Å: Chain D: D.107 Chain E: L.47, Y.50, A.56, T.57 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Y.50, E:T.57, E:T.57, D:D.107, D:D.107

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

PEG.3: 5 residues within 4Å: Chain C: F.24, A.25, S.26, N.127, Y.128 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.26 Water bridges: C:A.29, C:N.127 PEG.8: 7 residues within 4Å: Chain D: K.149, Q.177, S.178 Chain E: T.129, Q.160, T.180 Ligands: PEG.9 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:Q.160, D:K.149, D:S.178 Water bridges: D:D.150, D:D.150 PEG.9: 6 residues within 4Å: Chain D: L.176, Q.177, S.178, G.180 Chain E: Q.160 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.160 PEG.11: 7 residues within 4Å: Chain D: Q.39, V.92, Y.94 Chain E: Q.39, K.40, G.42, Q.43 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.42, E:Q.43 Water bridges: E:K.40, E:E.165, D:Q.39, D:Q.39, D:V.92, D:Y.94

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain C: R.134, E.142 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.134, C:R.134 Salt bridges: C:R.134 SO4.5: 2 residues within 4Å: Chain C: R.34, N.37 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.34 SO4.15: 4 residues within 4Å: Chain C: S.154 Chain D: S.25, G.26, L.27 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.26, C:S.154 Water bridges: D:N.76, D:N.76, D:N.76, D:N.76, C:S.154, C:S.154, C:S.154 SO4.16: 2 residues within 4Å: Chain D: K.123, G.124 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.124 Salt bridges: D:K.123 SO4.21: 6 residues within 4Å: Chain C: G.173, Q.175, N.178 Chain E: P.30, S.31 Ligands: CL.17 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:S.31, C:G.173, C:N.178 SO4.22: 4 residues within 4Å: Chain E: R.46, P.60, R.62, E.82 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.82 Water bridges: E:R.62 Salt bridges: E:K.40, E:R.46, E:R.62 SO4.23: 3 residues within 4Å: Chain E: P.8, G.9, T.10 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.9, E:T.10 SO4.24: 4 residues within 4Å: Chain E: Q.6, G.9, G.100, G.101 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.6 Water bridges: E:Q.6, E:Q.6, E:G.9 SO4.25: 4 residues within 4Å: Chain E: T.10, K.103, D.105, R.142 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:D.105 Water bridges: E:R.142, E:R.142, E:R.142 Salt bridges: E:K.103, E:R.142 SO4.26: 3 residues within 4Å: Chain E: R.18, S.77, R.78 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.77 Salt bridges: E:R.18, E:R.78 SO4.27: 4 residues within 4Å: Chain D: P.129 Chain E: S.121, D.122, E.123 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.122, E:E.123 Water bridges: E:P.120 SO4.28: 4 residues within 4Å: Chain E: P.60, D.61, R.62, R.78 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.62 Salt bridges: E:R.62, E:R.78

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.7: 7 residues within 4Å: Chain D: S.7, G.8, G.9, G.10, T.113, K.207, P.208 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.8, D:G.9, D:T.113 Water bridges: D:L.114, D:L.114 Salt bridges: D:K.207

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

CL.12: 5 residues within 4Å: Chain D: R.38, S.62, R.66, E.88, D.89 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain D: Y.151, E.154, P.155, V.156, A.174, L.184 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain D: S.62, V.63, K.64, R.66 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: Y.126 Chain E: P.30, S.31, S.32 Ligands: SO4.21 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain E: A.44 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain E: V.2, V.3, A.25, S.26, Q.27 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain E: P.141, R.142, Y.173 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dejnirattisai, W. et al., Antibody evasion by the P.1 strain of SARS-CoV-2. Cell (2021)

Release Date

2021-04-07

Peptides

EY6A Fab heavy chain: A
EY6A Fab light chain: B
Spike protein S1: C
COVOX-222 Fab heavy chain: D
COVOX-222 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

D
A

E
B

EY6A Fab heavy chain

EY6A Fab light chain

Spike protein S1

COVOX-222 Fab heavy chain

COVOX-222 Fab light chain

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