SMTL ID : 6p91.1

Structure of Lassa virus glycoprotein bound to Fab 18.5C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

6 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.1: 8 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, W.227 Chain D: W.24, I.64 Chain K: D.62 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.62 NAG-NAG-BMA-MAN.7: 14 residues within 4Å: Chain A: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, P.236, S.237 Chain D: N.106, S.108, G.132, S.133, Y.134 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.232, A:D.229 Hydrophobic interactions: D:Y.134 NAG-NAG-BMA-MAN.11: 8 residues within 4Å: Chain C: D.62 Chain E: E.76, T.77, N.79, M.80, W.227 Chain H: W.24, I.64 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.17: 14 residues within 4Å: Chain E: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, P.236, S.237 Chain H: N.106, S.108, G.132, S.133, Y.134 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:Q.232, E:D.229 Hydrophobic interactions: H:Y.134 NAG-NAG-BMA-MAN.21: 8 residues within 4Å: Chain G: D.62 Chain I: E.76, T.77, N.79, M.80, W.227 Chain L: W.24, I.64 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.62 NAG-NAG-BMA-MAN.27: 14 residues within 4Å: Chain I: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, P.236, S.237 Chain L: N.106, S.108, G.132, S.133, Y.134 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L Hydrogen bonds: I:Q.232, I:D.229 Hydrophobic interactions: L:Y.134

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

NAG-NAG.2: 4 residues within 4Å: Chain A: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: K.161, N.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain E: F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: K.161, N.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain I: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain I: N.99, E.100 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain I: F.117, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain I: K.161, N.224, T.225 No protein-ligand interaction detected (PLIP)

6 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.4: 4 residues within 4Å: Chain A: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 6 residues within 4Å: Chain A: Q.69 Chain D: K.32, C.33, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.31 NAG-NAG-BMA.14: 4 residues within 4Å: Chain E: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 6 residues within 4Å: Chain E: Q.69 Chain H: K.32, C.33, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:L.31 NAG-NAG-BMA.24: 4 residues within 4Å: Chain I: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 6 residues within 4Å: Chain I: Q.69 Chain L: K.32, C.33, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:L.31

3 x NAG- NAG- BMA- FUC: 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-FUC.9: 7 residues within 4Å: Chain C: D.2, I.3, Q.28, Y.92, G.94, S.95 Chain D: N.136 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.2, C:D.2, C:Q.28 NAG-NAG-BMA-FUC.19: 7 residues within 4Å: Chain G: D.2, I.3, Q.28, Y.92, G.94, S.95 Chain H: N.136 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.2, G:D.2, G:Q.28 NAG-NAG-BMA-FUC.29: 7 residues within 4Å: Chain K: D.2, I.3, Q.28, Y.92, G.94, S.95 Chain L: N.136 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.2, K:D.2, K:Q.28

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

NAG.10: 4 residues within 4Å: Chain A: C.207 Chain C: S.29, G.70 Chain D: N.131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.70 NAG.20: 4 residues within 4Å: Chain E: C.207 Chain G: S.29, G.70 Chain H: N.131 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.70 NAG.30: 4 residues within 4Å: Chain I: C.207 Chain K: S.29, G.70 Chain L: N.131 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:G.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hastie, K.M. et al., Convergent Structures Illuminate Features for Germline Antibody Binding and Pan-Lassa Virus Neutralization. Cell (2019)

Release Date

2019-08-21

Peptides

Pre-glycoprotein polyprotein GP complex: AEI
Fab 18.5C Antibody heavy chain: BFJ
Fab 18.5C Antibody light chain: CGK
Pre-glycoprotein polyprotein GP complex,Lassa virus glycoprotein, GP2 subunit: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
H

F
H

J
H

C
L

G
L

K
L

D
a

H
a

L
a

Pre-glycoprotein polyprotein GP complex

Fab 18.5C Antibody heavy chain

Fab 18.5C Antibody light chain

Pre-glycoprotein polyprotein GP complex,Lassa virus glycoprotein, GP2 subunit

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