SMTL ID : 4x1x.1

Crystal structure of RHDVb P domain in complex with Lewis Y

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 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.237, N.239, A.240, S.244, T.245, N.246 Chain B: W.126, S.129, N.130, G.131 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.237, A:S.244, A:S.244, A:N.246, B:S.129, B:S.129, A:T.245 Water bridges: A:N.239, A:T.245, A:N.246

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

EDO.2: 11 residues within 4Å: Chain A: T.136, V.138, Q.139, V.172, A.173 Chain B: T.136, V.138, Q.139, G.171, V.172, A.173 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.136, A:Q.139, A:A.173, B:T.136, B:Q.139, B:A.173 EDO.5: 6 residues within 4Å: Chain A: V.261, L.265 Chain B: P.11, V.12, V.16, P.258 No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain B: H.62, D.63, S.87, A.88, A.89, D.90, N.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.63, B:A.88, B:D.90

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

CL.3: 3 residues within 4Å: Chain A: N.127, N.130, A.132 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: Y.82, S.84, Q.163 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: N.91, P.98, D.99 Ligand excluded by PLIP

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