SMTL ID : 7sku.1

Nipah virus matrix protein in complex with PI(4,5)P2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.1: 23 residues within 4Å: Chain A: I.227, M.229, L.235, E.236, F.237, R.239, F.245, H.279, L.280, G.281, N.282, F.283, I.300, M.303, L.305, I.319, I.321, I.325, L.329, Q.332, M.333, L.339, R.374 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.235, A:F.245, A:F.245, A:F.283, A:I.321, A:L.329, A:Q.332, A:L.339 Hydrogen bonds: A:N.282, A:N.282, A:Q.332 Salt bridges: A:R.239, A:R.374 PIO.4: 21 residues within 4Å: Chain B: I.227, M.229, L.235, E.236, F.237, R.239, F.245, H.279, L.280, G.281, N.282, F.283, V.284, M.303, L.305, I.319, I.321, I.325, L.329, M.333, L.339 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.245, B:F.283, B:I.321, B:L.329, B:L.339 Hydrogen bonds: B:E.236, B:R.239, B:N.282, B:N.282

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.128, K.208 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.208, A:K.208 Salt bridges: A:R.128, A:K.208 SO4.3: 8 residues within 4Å: Chain A: T.92, P.93, G.94, A.95, N.96, Q.306, S.308, K.320 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.94, A:N.96, A:Q.306, A:S.308, A:S.308 Water bridges: A:N.96 Salt bridges: A:K.320 SO4.5: 4 residues within 4Å: Chain B: K.126, R.128, Q.205, K.208 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.205 Salt bridges: B:K.126, B:R.128 SO4.6: 4 residues within 4Å: Chain B: K.299, S.326, K.327, R.328 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.327 Salt bridges: B:K.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Norris, M.J. et al., Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerization. Sci Adv (2022)

Release Date

2022-08-24

Peptides

Matrix protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Matrix protein

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