SMTL ID : 5oyl.1

VSV G CR2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 1 residues within 4Å: Chain A: N.163 No protein-ligand interaction detected (PLIP) NAG.2: 1 residues within 4Å: Chain A: S.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.377, A:S.377 NAG.3: 1 residues within 4Å: Chain A: N.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.320

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.201, G.202, T.214, G.216 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.201 CA.12: 6 residues within 4Å: Chain B: W.27, D.30, Q.32, D.34, D.40, E.41 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:W.27, B:D.30, B:Q.32, B:D.34, B:D.40, B:E.41

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: E.255, G.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.256 Water bridges: A:P.254 GOL.6: 5 residues within 4Å: Chain A: I.339, L.340, S.341, S.378, G.379 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.339 GOL.7: 5 residues within 4Å: Chain A: N.13, K.15, P.131, H.132, H.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.13, A:N.13, A:H.133, A:H.133 GOL.8: 5 residues within 4Å: Chain A: S.27, S.28, E.276, D.280, K.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.28, A:K.308 Water bridges: A:S.28, A:E.276 GOL.9: 9 residues within 4Å: Chain A: V.5, F.6, S.303, N.371, V.373, F.382, P.383, L.384, Y.385 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.5, A:N.371, A:L.384 GOL.10: 5 residues within 4Å: Chain A: Y.385, M.386, I.387, G.388, H.389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.386 GOL.11: 1 residues within 4Å: Chain B: R.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.21, B:R.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nikolic, J. et al., Structural basis for the recognition of LDL-receptor family members by VSV glycoprotein. Nat Commun (2018)

Release Date

2018-03-21

Peptides

Glycoprotein: A
Low-density lipoprotein receptor: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Glycoprotein

Low-density lipoprotein receptor

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