SMTL ID : 6yrq.1

Crystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at pH 4.6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x U- U- U- A: RNA (5'-R(*AP*UP*UP*UP*A)-3')(Non-covalent)

U-U-U-A.1: 19 residues within 4Å: Chain A: P.14, Q.54, R.55, D.57 Chain C: T.6, V.7, F.8, C.9, 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 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 D: P.14, Q.54, R.55, D.57 Protein-ligand interaction information (PLIP) not available U-U-U-A.3: 19 residues within 4Å: Chain B: T.6, V.7, F.8, C.9, 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 U-U-U-A.4: 19 residues within 4Å: Chain B: P.14, Q.54, R.55, D.57 Chain D: T.6, V.7, F.8, C.9, 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

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

NAG-NAG.5: 3 residues within 4Å: Chain C: N.28, N.65, G.66 No protein-ligand interaction detected (PLIP)

1 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.6: 3 residues within 4Å: Chain D: F.27, N.28, N.65 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: F.27, N.28, G.66 No protein-ligand interaction detected (PLIP)

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 5 residues within 4Å: Chain A: F.8, T.10, S.17 Chain D: A.12, S.17 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.12 MPD.9: 5 residues within 4Å: Chain B: F.8, T.10, S.17 Chain C: A.12, S.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.12 Hydrogen bonds: B:F.8 MPD.10: 5 residues within 4Å: Chain A: A.12, S.17 Chain C: F.8, T.10, S.17 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.12 Hydrogen bonds: C:S.17, C:S.17 MPD.11: 6 residues within 4Å: Chain B: A.12, S.17, I.52 Chain D: F.8, T.10, S.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.12 Hydrogen bonds: B:S.17

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Envelope polyprotein

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