SMTL ID : 7nx7.1

Crystal structure of the K417N 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 2.30 Å

Oligo State

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

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain C: T.53, G.81, D.82, G.181, Y.185 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.53, C:T.53, C:D.82, C:D.82 GOL.6: 8 residues within 4Å: Chain C: N.94, L.132 Chain D: Y.33, Y.52, E.99, S.101, N.104 Chain E: Y.92 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.33, D:Y.52, D:S.101 Water bridges: C:N.94, C:N.94, C:N.94 GOL.11: 6 residues within 4Å: Chain D: S.167, G.168, V.169 Chain E: D.167, S.168, K.169 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:D.167, D:G.168

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

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

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

SO4.3: 3 residues within 4Å: Chain C: R.134, K.139, E.142 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.142 Water bridges: C:R.134, C:R.134 Salt bridges: C:R.134, C:K.139 SO4.4: 2 residues within 4Å: Chain C: R.34, N.37 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.34, C:R.34 Salt bridges: C:R.34 SO4.5: 2 residues within 4Å: Chain C: K.121, N.127 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.127 Salt bridges: C:K.121 SO4.7: 5 residues within 4Å: Chain C: S.154 Chain D: S.25, G.26, L.27, N.76 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.26, D:L.27, D:N.76, C:S.154 SO4.8: 5 residues within 4Å: Chain D: S.7, G.8, G.9, T.113, K.207 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.8, D:G.9, D:T.113 SO4.9: 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 SO4.13: 1 residues within 4Å: Chain E: R.211 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.211 SO4.14: 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 SO4.15: 3 residues within 4Å: Chain E: K.103, D.105, R.142 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.105 Water bridges: E:R.142 Salt bridges: E:K.103, E:R.142 SO4.16: 4 residues within 4Å: Chain D: P.129 Chain E: S.121, D.122, E.123 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.122, E:E.123 SO4.17: 4 residues within 4Å: Chain E: P.60, D.61, R.62, R.78 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.61, E:R.62 Salt bridges: E:R.62, E:R.78 SO4.18: 3 residues within 4Å: Chain E: R.18, S.77, R.78 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.78 Salt bridges: E:R.18 SO4.19: 4 residues within 4Å: Chain E: K.40, R.46, P.60, R.62 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:K.40, E:R.46, E:R.62

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

CL.10: 6 residues within 4Å: Chain D: Y.151, E.154, P.155, V.156, A.174, L.184 Ligand excluded by PLIP

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

CIT.12: 10 residues within 4Å: Chain C: G.123, Y.126, Y.172, G.173, Q.175, N.178 Chain E: P.30, S.31, S.32, S.68 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:G.123, C:G.173, C:N.178, E:S.31, E:S.31, E:S.32

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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