SMTL ID : 7s5q.1

Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibodies CS44 and COVA1-16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.88 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: 5 residues within 4Å: Chain A: G.21, F.24, N.25, L.50 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.24, A:L.50 Hydrogen bonds: A:N.25

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

EDO.2: 7 residues within 4Å: Chain A: Y.62, R.90, A.93, Q.96 Chain D: P.100, R.101, Y.115 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Y.62, A:R.90, D:R.101, D:Y.115 EDO.3: 4 residues within 4Å: Chain A: T.112, F.146, S.196, F.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.112 EDO.11: 2 residues within 4Å: Chain D: S.25, G.26 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.26 EDO.15: 9 residues within 4Å: Chain D: F.182, P.183, V.185, L.194, S.195 Chain E: Q.160, S.162, S.176, T.178 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:S.195, E:Q.160, E:S.162, E:S.176 EDO.16: 3 residues within 4Å: Chain E: P.8, S.9, S.10 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.9, E:S.10, E:S.10

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

SO4.4: 4 residues within 4Å: Chain A: T.182, Y.183, G.184, Y.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.182, A:Y.183, A:G.184 SO4.5: 3 residues within 4Å: Chain A: G.128, G.129, Y.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.128 Water bridges: A:G.128 Salt bridges: A:K.126 SO4.6: 3 residues within 4Å: Chain A: S.125, K.126, V.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.127 Water bridges: A:G.128 SO4.7: 6 residues within 4Å: Chain A: F.24, N.25, S.55, F.56, W.118 Ligands: NAG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.55 SO4.8: 2 residues within 4Å: Chain A: K.126, N.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.132 Salt bridges: A:K.126 SO4.9: 3 residues within 4Å: Chain A: Y.51, N.52, N.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.51, A:N.52, A:N.70 SO4.10: 4 residues within 4Å: Chain B: I.27, T.28, F.29, T.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.29, B:T.30, B:T.30, B:S.77 SO4.12: 4 residues within 4Å: Chain A: G.63 Chain D: R.101, N.102, Y.110 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.63, D:N.102 Water bridges: D:N.102 Salt bridges: D:R.101 SO4.13: 1 residues within 4Å: Chain D: R.72 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.72 SO4.14: 4 residues within 4Å: Chain D: V.2, Q.117, H.118, W.119 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.2, D:W.119 Salt bridges: D:H.118 SO4.17: 2 residues within 4Å: Chain E: K.190, R.211 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:K.190, E:R.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reincke, S.M. et al., SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies. Science (2022)

Release Date

2022-03-09

Peptides

Spike protein S1: A
CS44 Heavy chain: B
CS44 Light chain: C
COVA1-16 Heavy chain: D
COVA1-16 Light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike protein S1

CS44 Heavy chain

CS44 Light chain

COVA1-16 Heavy chain

COVA1-16 Light chain

Related Entries With Identical Sequence