SMTL ID : 5w4d.1 (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

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

EDO.1: 4 residues within 4Å: Chain A: D.107, L.108, M.126, L.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.107, A:D.107 EDO.2: 2 residues within 4Å: Chain A: Y.154, D.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.154 Water bridges: A:Y.154 EDO.8: 6 residues within 4Å: Chain B: N.21, Y.25, N.41, Q.62, M.63, P.66 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.21, B:N.21 Water bridges: B:N.41, B:N.41 EDO.9: 2 residues within 4Å: Chain B: S.56, D.58 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.58, B:D.58

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

PGE.3: 8 residues within 4Å: Chain A: S.69, D.70, S.71, I.74, D.98, L.99, F.102, L.104 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.71, A:S.71

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

PEG.4: 6 residues within 4Å: Chain A: K.120, K.121, N.124, N.149, E.155 Ligands: CL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.121 Water bridges: A:E.155 PEG.7: 5 residues within 4Å: Chain A: N.38, K.39, A.40, S.42, K.53 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.40 PEG.11: 8 residues within 4Å: Chain B: M.1, F.11, P.20, N.21, L.24, P.66, S.69, T.73 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.68, B:T.73 PEG.12: 4 residues within 4Å: Chain A: L.125 Chain B: E.152, Y.154, D.185 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.154, B:Y.154, B:D.185

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

PG4.5: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.179

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

CL.6: 5 residues within 4Å: Chain A: N.124, I.145, K.146, N.149 Ligands: PEG.4 Ligand excluded by PLIP

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 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:N.4, B:T.76, B:T.76

1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.13: 11 residues within 4Å: Chain B: Y.46, K.54, P.55, V.57, I.60, D.87, F.88, K.177, I.178, L.179, G.180 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.54

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
A

B
C

P-granule scaffold protein

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