SMTL ID : 6y65.2 (1 other biounit)

Structure of apo Goose Hemorrhagic Polyomavirus VP1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-pentamer

Ligands

47 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: T.58, V.59, A.60, D.66, V.67, P.68 Chain D: H.117 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: H.117 Chain E: T.58, V.59, A.60, D.66, V.67, P.68 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: G.125, G.126, Y.127 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: H.139, F.141, F.210, T.212 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: N.137, H.139, T.212, P.221, V.222 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: L.86, N.87, M.90, G.245, D.246 Ligands: EDO.8 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: C.78, A.79, R.80, L.186, D.187, Y.249 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: N.87, L.96, C.243, K.244, G.245, D.246 Ligands: EDO.6 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: R.30, T.92, E.94, L.284 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: T.49, S.54, Q.55, H.268 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: H.117 Chain C: T.58, V.59, A.60, D.66, V.67, P.68 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain B: T.58, V.59, A.60, D.66, V.67, P.68 Chain E: H.117 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain B: G.126, Y.127 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: H.139, F.141, F.210, T.212 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: N.137, H.139, T.212, T.214, P.221, V.222 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: L.86, N.87, G.245, D.246 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain B: N.87, I.95, L.96, M.97, C.243, K.244, G.245, D.246 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: Y.161, P.162, V.165, V.166, A.167 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: R.30, T.92, E.94, L.284 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: C.78, D.187, K.188, D.189 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: T.49, F.53, S.54, Q.55, H.268 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: T.49, D.50 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain C: H.117 Chain D: T.58, V.59, A.60, D.66, V.67, P.68 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain C: G.125, G.126, Y.127 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain C: H.139, F.141, F.210, T.212 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: N.137, H.139, T.212, T.214, P.221, V.222 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain C: Y.161, P.162, S.163, V.165, V.166, A.167 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: V.166, A.167, K.183, A.184, Y.192, W.197 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: R.30, T.92, E.94, L.96, L.284 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: M.97, V.285, R.286, N.287 Ligand excluded by PLIP EDO.35: 9 residues within 4Å: Chain C: M.21, E.205, N.206, R.208, D.235, V.239, G.240, P.241, L.242 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: T.49, F.53, S.54, H.268 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain D: G.125, G.126, Y.127 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain D: H.139, F.141, F.210, G.211, T.212 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain D: N.137, H.139, T.212, T.214, P.221, V.222 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: M.85, L.86, N.87, M.90, G.245, D.246 Ligands: EDO.44 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain D: N.87, L.96, M.97, C.243, G.245, D.246 Ligands: EDO.43, EDO.47 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain D: V.166, A.167, P.169, K.183, A.184, W.197 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: R.30, T.92, E.94, L.284 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain D: I.24, R.286, N.287 Ligands: EDO.44 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain E: G.126, Y.127 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain E: H.139, F.141, F.210, G.211, T.212 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain E: N.137, H.139, P.221, V.222 Ligand excluded by PLIP EDO.54: 6 residues within 4Å: Chain E: M.85, L.86, N.87, G.245, D.246 Ligands: EDO.55 Ligand excluded by PLIP EDO.55: 7 residues within 4Å: Chain E: N.87, L.96, C.243, K.244, G.245, D.246 Ligands: EDO.54 Ligand excluded by PLIP EDO.56: 7 residues within 4Å: Chain E: V.166, A.167, P.169, K.183, A.184, Y.192, W.197 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain E: T.49, F.53, S.54, H.268 Ligand excluded by PLIP

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 2 residues within 4Å: Chain A: N.44, R.46 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: V.29, R.30, T.31 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: N.44, R.46 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: R.30, T.31 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain C: N.44, R.46 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain C: R.30, T.31 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain D: N.44, R.46 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain D: R.30, T.31 Ligand excluded by PLIP CL.58: 2 residues within 4Å: Chain E: R.30, T.31 Ligand excluded by PLIP

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.39: 3 residues within 4Å: Chain A: Y.263, S.264 Chain D: Y.127 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:S.264 pi-Stacking: D:Y.127 IMD.50: 3 residues within 4Å: Chain B: Y.263, S.264 Chain E: Y.127 1 PLIP interactions: 1 interactions with chain E pi-Stacking: E:Y.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroh, L.J. et al., Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family. Mbio (2020)

Release Date

2020-07-08

Peptides

Capsid protein VP1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
FFF

B
GGG

C
HHH

D
III

E
JJJ

Capsid protein VP1

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