SMTL ID : 4x1z.1

Crystal structure of RHDVb P domain in complex with H type 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-dimer

Ligands

2 x NDG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-functional Binders)

NDG-GAL-FUC.1: 10 residues within 4Å: Chain A: D.235, N.237, A.238, S.242, T.243, N.244 Chain B: W.124, S.127, N.128, G.129 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.235, A:S.242, A:S.242, A:N.244, B:S.127, B:S.127, A:T.243, A:T.243 Water bridges: A:N.237, A:T.243, A:N.244 NDG-GAL-FUC.2: 10 residues within 4Å: Chain A: W.124, S.127, N.128, G.129 Chain B: D.235, N.237, A.238, S.242, T.243, N.244 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.235, B:S.242, B:S.242, B:N.244, A:S.127, A:S.127, A:S.127, B:T.243 Water bridges: B:T.243, A:D.61, B:N.244

14 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: R.54, A.56, A.57 Chain B: R.231 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.54, A:R.54, A:A.57, A:A.57, B:R.231 Water bridges: B:R.231 NA.4: 2 residues within 4Å: Chain A: T.198, Y.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.199 Water bridges: A:Q.202 NA.5: 5 residues within 4Å: Chain A: P.9, V.10, V.14, G.15, P.256 No protein-ligand interaction detected (PLIP) NA.6: 5 residues within 4Å: Chain A: F.104, P.106, F.107, P.151, K.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.107, A:F.107, A:K.165 NA.7: 4 residues within 4Å: Chain A: I.94, T.157, S.158, P.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.157, A:T.157 NA.8: 2 residues within 4Å: Chain A: N.42, N.44 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.42, A:N.44, A:S.46, A:S.46 NA.9: 7 residues within 4Å: Chain A: T.134, V.136, Q.137, V.170, A.171 Chain B: Q.137 Ligands: NA.16 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.136, A:A.171 Water bridges: B:Q.137 NA.10: 2 residues within 4Å: Chain B: T.198, Y.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.199 Water bridges: B:Q.202 NA.11: 5 residues within 4Å: Chain B: P.9, V.10, V.14, G.15, P.256 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.9 NA.12: 4 residues within 4Å: Chain B: I.94, T.157, S.158, P.210 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.157 NA.13: 5 residues within 4Å: Chain B: F.104, P.106, F.107, P.151, K.165 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.107, B:F.107, B:K.165 NA.14: 4 residues within 4Å: Chain B: D.88, N.89, P.96, D.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.88, B:D.97 NA.15: 4 residues within 4Å: Chain A: R.231 Chain B: R.54, A.56, A.57 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.54, B:R.54, B:A.57, B:A.57, A:R.231 Water bridges: A:R.231 NA.16: 8 residues within 4Å: Chain A: Q.137 Chain B: T.134, T.135, V.136, Q.137, V.170, A.171 Ligands: NA.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.136, B:A.171 Water bridges: A:Q.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leuthold, M.M. et al., Structural analysis of a rabbit hemorrhagic disease virus binding to histo-blood group antigens. J.Virol. (2015)

Release Date

2015-01-14

Peptides

VP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VP1

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