SMTL ID : 6yrb.1

Crystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at pH 7.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-octamer

Ligands

16 x A- U- U- U- A: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')(Non-functional Binders)(Non-covalent)

A-U-U-U-A.1: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available A-U-U-U-A.2: 20 residues within 4Å: Chain A: T.6, V.7, F.8, C.9, Q.67, K.69, V.70, I.71, L.72, T.75, L.76, I.78, G.79, I.82, V.101, V.105 Chain C: P.14, Q.54, R.55, D.57 Protein-ligand interaction information (PLIP) not available A-U-U-U-A.7: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available A-U-U-U-A.8: 20 residues within 4Å: Chain B: T.6, V.7, F.8, C.9, Q.67, K.69, V.70, I.71, L.72, T.75, L.76, I.78, G.79, I.82, V.101, V.105 Chain D: P.14, Q.54, R.55, D.57 Protein-ligand interaction information (PLIP) not available A-U-U-U-A.13: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available A-U-U-U-A.14: 20 residues within 4Å: Chain B: P.14, Q.54, R.55, D.57 Chain C: T.6, V.7, F.8, C.9, Q.67, K.69, V.70, I.71, L.72, T.75, L.76, I.78, G.79, I.82, V.101, V.105 Protein-ligand interaction information (PLIP) not available A-U-U-U-A.19: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available A-U-U-U-A.20: 20 residues within 4Å: Chain A: P.14, Q.54, R.55, D.57 Chain D: T.6, V.7, F.8, C.9, Q.67, K.69, V.70, I.71, L.72, T.75, L.76, I.78, G.79, I.82, V.101, V.105 Protein-ligand interaction information (PLIP) not available A-U-U-U-A.25: 20 residues within 4Å: Chain E: T.6, V.7, F.8, C.9, Q.67, K.69, V.70, I.71, L.72, T.75, L.76, I.78, G.79, I.82, V.101, V.105 Chain H: P.14, Q.54, R.55, D.57 Protein-ligand interaction information (PLIP) not available A-U-U-U-A.26: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available A-U-U-U-A.30: 20 residues within 4Å: Chain F: T.6, V.7, F.8, C.9, Q.67, K.69, V.70, I.71, L.72, T.75, L.76, I.78, G.79, I.82, V.101, V.105 Chain G: P.14, Q.54, R.55, D.57 Protein-ligand interaction information (PLIP) not available A-U-U-U-A.31: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available A-U-U-U-A.35: 20 residues within 4Å: Chain E: P.14, Q.54, R.55, D.57 Chain G: T.6, V.7, F.8, C.9, Q.67, K.69, V.70, I.71, L.72, T.75, L.76, I.78, G.79, I.82, V.101, V.105 Protein-ligand interaction information (PLIP) not available A-U-U-U-A.36: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available A-U-U-U-A.40: 20 residues within 4Å: Chain F: P.14, Q.54, R.55, D.57 Chain H: T.6, V.7, F.8, C.9, Q.67, K.69, V.70, I.71, L.72, T.75, L.76, I.78, G.79, I.82, V.101, V.105 Protein-ligand interaction information (PLIP) not available A-U-U-U-A.41: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available

4 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.3: 4 residues within 4Å: Chain A: F.27, N.28, N.65, G.66 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.27 NAG-NAG-BMA-FUC.9: 4 residues within 4Å: Chain B: F.27, N.28, N.65, G.66 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.27 NAG-NAG-BMA-FUC.15: 4 residues within 4Å: Chain C: F.27, N.28, N.65, G.66 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.27 NAG-NAG-BMA-FUC.21: 4 residues within 4Å: Chain D: F.27, N.28, N.65, G.66 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.27

24 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 1 residues within 4Å: Chain A: G.66 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: M.92, D.94 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: K.68 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain B: G.66 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain B: M.92, D.94 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain B: K.68 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain C: G.66 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain C: M.92, D.94 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain C: K.68 Ligand excluded by PLIP IOD.22: 1 residues within 4Å: Chain D: G.66 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain D: M.92, D.94 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain D: K.68 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain E: M.92, P.93, D.94 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain E: P.32 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain E: S.98, E.102 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain F: M.92, P.93, D.94 Ligand excluded by PLIP IOD.33: 1 residues within 4Å: Chain F: P.32 Ligand excluded by PLIP IOD.34: 2 residues within 4Å: Chain F: S.98, E.102 Ligand excluded by PLIP IOD.37: 3 residues within 4Å: Chain G: M.92, P.93, D.94 Ligand excluded by PLIP IOD.38: 1 residues within 4Å: Chain G: P.32 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain G: S.98, E.102 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain H: M.92, P.93, D.94 Ligand excluded by PLIP IOD.43: 1 residues within 4Å: Chain H: P.32 Ligand excluded by PLIP IOD.44: 2 residues within 4Å: Chain H: S.98, E.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Serris, A. et al., The Hantavirus Surface Glycoprotein Lattice and Its Fusion Control Mechanism. Cell (2020)

Release Date

2020-10-14

Peptides

Envelope polyprotein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
B

F
B

G
B

H
B

Envelope polyprotein

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