SMTL ID : 6nb7.1

SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

21 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 2 residues within 4Å: Chain A: N.128, K.129 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: N.138, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 1 residues within 4Å: Chain A: N.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: N.337, K.585 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: G.345, N.349, T.378 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: N.621, Q.649 Chain C: I.851 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain A: N.718, K.930 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain B: N.128, K.129 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 1 residues within 4Å: Chain B: N.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 2 residues within 4Å: Chain B: N.337, K.585 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 2 residues within 4Å: Chain B: F.348, N.349 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 5 residues within 4Å: Chain A: I.851, C.852 Chain B: N.621, T.623, Q.649 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain B: N.718, F.719, Q.923, Q.927 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.927 NAG-NAG-BMA.22: 3 residues within 4Å: Chain B: E.1073, R.1074, N.1075 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 1 residues within 4Å: Chain C: N.128 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 2 residues within 4Å: Chain C: S.124, N.246 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 4 residues within 4Å: Chain C: N.337, K.585, T.586, S.587 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 4 residues within 4Å: Chain C: F.344, G.345, N.349, S.377 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 3 residues within 4Å: Chain B: I.851 Chain C: N.621, Q.649 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 5 residues within 4Å: Chain C: I.706, A.707, E.1073, R.1074, N.1075 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 2 residues within 4Å: Chain C: I.1133, N.1135 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.7: 1 residues within 4Å: Chain A: N.710 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 5 residues within 4Å: Chain A: K.796, Y.797, N.802, S.804, Q.805 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 4 residues within 4Å: Chain A: A.707, E.1073, R.1074, N.1075 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.707 NAG-NAG-BMA-MAN-MAN.12: 2 residues within 4Å: Chain A: I.1133, N.1135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.21: 4 residues within 4Å: Chain B: Y.797, N.802, S.804, Q.805 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.34: 5 residues within 4Å: Chain C: K.796, Y.797, N.802, S.804, Q.805 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.11: 4 residues within 4Å: Chain A: R.1074, N.1099, G.1100, F.1104 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.36: 3 residues within 4Å: Chain C: N.1099, G.1100, F.1104 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.14: 2 residues within 4Å: Chain B: N.138, T.169 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain B: N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.138, T.140, T.169 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain A: R.563 Chain C: N.288 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain C: N.710, N.711 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 1 residues within 4Å: Chain C: N.718 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.23: 4 residues within 4Å: Chain B: N.1099, G.1100, S.1102, F.1104 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 2 residues within 4Å: Chain B: I.1133, N.1135 No protein-ligand interaction detected (PLIP)

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

NAG.38: 1 residues within 4Å: Chain A: N.376 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: S.83, N.84 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.92 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain A: N.177 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: G.244, I.245, N.246 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain A: N.608, A.609 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: S.372, N.376 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.48, T.50 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.84 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.177 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.246 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain B: N.608, A.609 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.376 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.84 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.92 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.608, A.609 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walls, A.C. et al., Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion. Cell (2019)

Release Date

2019-02-06

Peptides

Spike glycoprotein: ABC
S230 heavy chain: DFG
S230 light chain: EHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
G

G
H

E
E

H
I

I
L

Spike glycoprotein

S230 heavy chain

S230 light chain

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