SMTL ID : 6p95.1

Structure of Lassa virus glycoprotein in complex with Fab 25.6A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

4 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, W.227 Chain I: N.63 Chain J: R.23, W.24, I.64 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:I.64 NAG-NAG-BMA.4: 8 residues within 4Å: Chain B: E.76, T.77, N.79, M.80 Chain E: N.63 Chain K: R.23, W.24, I.64 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.64 NAG-NAG-BMA.7: 7 residues within 4Å: Chain C: E.76, T.77, N.79, M.80, W.227 Chain L: W.24, I.64 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:I.64 NAG-NAG-BMA.9: 4 residues within 4Å: Chain C: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP)

7 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: 3 residues within 4Å: Chain A: K.88, N.89, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: K.88, N.89, S.91, H.92 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 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: G.159, K.161, N.224, T.225 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: Q.69 Chain K: C.33, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain C: Q.69 Chain L: C.33, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP)

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.6: 4 residues within 4Å: Chain B: N.109, S.216, Y.217, Q.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 14 residues within 4Å: Chain B: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, P.236, S.237 Chain K: N.106, S.108, G.132, Y.134 Ligands: NAG-NAG-FUC.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.232, B:D.229 NAG-NAG-BMA-MAN.17: 13 residues within 4Å: Chain C: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain L: N.106, S.108, G.132, Y.134 Ligands: NAG-NAG-FUC.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.232, C:D.229, C:Q.232

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.11: 13 residues within 4Å: Chain A: G.197, D.229, C.231, Q.232, F.233, S.234, R.235, S.237 Chain J: N.106, S.108, G.132, Y.134 Ligands: NAG-NAG-FUC.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.232

1 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.12: 5 residues within 4Å: Chain A: Q.69 Chain J: C.33, Y.112, N.114, T.121 No protein-ligand interaction detected (PLIP)

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.13: 5 residues within 4Å: Chain E: T.96 Chain J: K.109, Y.134, N.136 Ligands: NAG-NAG-BMA-MAN-MAN.11 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:Y.134 Hydrogen bonds: J:K.109, J:K.109 NAG-NAG-FUC.16: 6 residues within 4Å: Chain G: T.96, N.97 Chain K: K.109, Y.134, N.136 Ligands: NAG-NAG-BMA-MAN.14 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:Y.134 Hydrogen bonds: K:K.109, K:K.109 NAG-NAG-FUC.19: 6 residues within 4Å: Chain I: T.96, N.97 Chain L: K.109, Y.134, N.136 Ligands: NAG-NAG-BMA-MAN.17 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:Y.134 Hydrogen bonds: L:K.109, L:K.109

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

NAG.20: 3 residues within 4Å: Chain A: M.80, N.99, E.100 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.100 Hydrogen bonds: A:E.100, A:E.100 NAG.21: 6 residues within 4Å: Chain A: I.113, 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.22: 4 residues within 4Å: Chain A: G.159, K.161, N.224, T.225 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.225 Hydrogen bonds: A:N.224 NAG.23: 3 residues within 4Å: Chain B: M.80, N.99, E.100 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.100 Hydrogen bonds: B:N.99, B:E.100, B:E.100 NAG.24: 4 residues within 4Å: Chain B: I.113, Q.165, N.167, Y.219 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.219 Hydrogen bonds: B:N.167, B:Y.219, B:Y.219 NAG.25: 4 residues within 4Å: Chain B: G.159, K.161, N.224, T.225 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.225 Hydrogen bonds: B:N.224 NAG.26: 3 residues within 4Å: Chain C: M.80, N.99, E.100 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.100 Hydrogen bonds: C:N.99, C:E.100, C:E.100 NAG.27: 6 residues within 4Å: Chain C: I.113, Q.165, N.167, S.169, H.170, 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.28: 4 residues within 4Å: Chain A: Y.200 Chain E: G.31, N.72 Chain J: N.131 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:Y.200 Hydrogen bonds: E:N.72

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

2019-09-11

Peptides

Pre-glycoprotein polyprotein GP complex: ABC
FAB Antibody heavy chain: DFH
FAB Antibody light chain: EGI
Pre-glycoprotein polyprotein GP complex: JKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
L

J
a

K
b

L
c

Pre-glycoprotein polyprotein GP complex

FAB Antibody heavy chain

FAB Antibody light chain

Pre-glycoprotein polyprotein GP complex

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