SMTL ID : 5w4d.2 (1 other biounit)

C. japonica N-domain, Selenomethionine mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 3 residues within 4Å: Chain A: N.28, N.29, E.31 No protein-ligand interaction detected (PLIP)

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

EDO.2: 6 residues within 4Å: Chain A: D.70, S.71, I.74, L.99, F.102, L.104 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.71 EDO.8: 4 residues within 4Å: Chain B: N.4, S.71, L.75, L.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.4

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 9 residues within 4Å: Chain A: N.4, K.5, R.6, Y.17, L.75, T.76, D.79, H.106, D.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.4, A:D.79 IMD.4: 3 residues within 4Å: Chain A: E.152, Y.154, D.185 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.154 pi-Stacking: A:Y.154 IMD.5: 3 residues within 4Å: Chain A: E.151, E.152, N.153 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.153 IMD.9: 9 residues within 4Å: Chain B: N.4, K.5, R.6, Y.17, L.75, T.76, D.79, H.106, D.107 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.75, B:D.107 Water bridges: B:R.6

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 11 residues within 4Å: Chain A: Y.46, K.54, P.55, V.57, I.60, D.87, F.88, K.177, I.178, L.179, G.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.178, A:I.178 Water bridges: A:K.54 PGE.10: 12 residues within 4Å: Chain B: Y.46, K.54, P.55, V.57, I.60, L.84, D.87, F.88, K.177, I.178, L.179, G.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.87 Water bridges: B:Y.46

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 8 residues within 4Å: Chain A: M.1, T.3, V.9, F.11, P.20, G.72, T.73, T.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aoki, S.T. et al., C. elegans germ granules require both assembly and localized regulators for mRNA repression. Nat Commun (2021)

Release Date

2018-06-13

Peptides

P-granule scaffold protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

P-granule scaffold protein

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