SMTL ID : 5vk2.1

Structural basis for antibody-mediated neutralization of Lassa virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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: 9 residues within 4Å: Chain A: E.76, T.77, N.79, M.80, N.99, W.227 Chain B: W.24, I.64 Chain H: N.63 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:W.24, H:N.63 Hydrophobic interactions: B:I.64 NAG-NAG-BMA.13: 9 residues within 4Å: Chain E: E.76, T.77, N.79, M.80, N.99, W.227 Chain F: R.23, W.24, I.64 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:W.24 Hydrophobic interactions: F:I.64 NAG-NAG-BMA.17: 6 residues within 4Å: Chain E: I.113, K.116, Q.165, N.167, S.169, Y.219 No protein-ligand interaction detected (PLIP)

11 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.109, S.216 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: H.115, N.119, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 9 residues within 4Å: Chain A: Q.69 Chain B: E.30, L.31, K.32, C.33, F.34, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.31 NAG-NAG.8: 7 residues within 4Å: Chain C: E.76, T.77, N.79, N.99, W.227 Chain D: W.24, I.64 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.64 NAG-NAG.9: 4 residues within 4Å: Chain C: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: H.115, N.119, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 9 residues within 4Å: Chain E: Q.69 Chain F: E.30, L.31, K.32, C.33, F.34, Y.112, N.114, T.121 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.31

3 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.5: 13 residues within 4Å: Chain A: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain B: N.106, S.108, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.232, A:D.229 NAG-NAG-BMA-MAN.11: 13 residues within 4Å: Chain C: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain D: N.106, S.108, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.232, C:C.231 NAG-NAG-BMA-MAN.18: 13 residues within 4Å: Chain E: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain F: N.106, S.108, G.132, S.133, Y.134 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.232, E:D.229

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.7: 5 residues within 4Å: Chain B: K.109, Y.134, N.136 Chain L: I.96, H.97 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.134 Hydrogen bonds: B:K.109 NAG-NAG-FUC.12: 5 residues within 4Å: Chain D: K.109, Y.134, N.136 Chain J: I.96, H.97 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.134 Hydrogen bonds: D:K.109 NAG-NAG-FUC.20: 5 residues within 4Å: Chain F: K.109, Y.134, N.136 Chain H: I.96, H.97 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.134 Hydrogen bonds: F:K.109

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

NAG.21: 1 residues within 4Å: Chain A: N.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.99 NAG.22: 7 residues within 4Å: Chain A: I.113, K.116, Q.165, N.167, S.169, H.170, Y.219 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.219 Hydrogen bonds: A:N.167, A:Y.219, A:Y.219 NAG.23: 3 residues within 4Å: Chain A: K.161, N.224, T.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.161, A:N.224, A:T.226 NAG.24: 3 residues within 4Å: Chain B: N.131 Chain L: G.27, G.31 No protein-ligand interaction detected (PLIP) NAG.25: 1 residues within 4Å: Chain C: N.99 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.99 NAG.26: 6 residues within 4Å: Chain C: I.113, K.116, Q.165, N.167, S.169, Y.219 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.219 Hydrogen bonds: C:N.167, C:Y.219, C:Y.219 NAG.27: 4 residues within 4Å: Chain C: K.161, N.224, T.225, T.226 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.161, C:N.224 NAG.28: 7 residues within 4Å: Chain C: Q.69 Chain D: K.32, C.33, F.34, Y.112, N.114, T.121 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.34, D:T.121 NAG.29: 2 residues within 4Å: Chain E: N.99, E.100 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.99 NAG.30: 4 residues within 4Å: Chain E: K.161, N.224, T.225, T.226 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.224 NAG.31: 2 residues within 4Å: Chain F: N.131 Chain H: G.31 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hastie, K.M. et al., Structural basis for antibody-mediated neutralization of Lassa virus. Science (2017)

Release Date

2017-05-31

Peptides

Pre-glycoprotein polyprotein GP complex: ACE
Pre-glycoprotein polyprotein GP complex: BDF
Fab 37.7H heavy chain: GIK
Fab 37.7H light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

B
a

D
b

F
c

G
D

I
F

K
H

H
E

J
G

L
L

Pre-glycoprotein polyprotein GP complex

Pre-glycoprotein polyprotein GP complex

Fab 37.7H heavy chain

Fab 37.7H light chain

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