SMTL ID : 5w4a.1 (1 other biounit)

C. japonica N-domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: E.7, E.136 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.136 EDO.2: 5 residues within 4Å: Chain A: R.6, D.107, L.108, M.126, L.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.107 EDO.3: 6 residues within 4Å: Chain A: K.134, T.135, E.136, K.139, L.166 Ligands: EDO.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.134 Water bridges: A:E.136, A:E.136, A:K.139, B:G.165 EDO.4: 9 residues within 4Å: Chain A: N.4, K.5, R.6, Y.17, G.72, L.75, T.76, D.79, H.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.17, A:T.76, A:D.79, A:H.106 Water bridges: A:E.7 EDO.7: 8 residues within 4Å: Chain B: V.57, I.60, L.84, D.87, F.88, I.178, L.179 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain B: Y.154, D.185 No protein-ligand interaction detected (PLIP) EDO.9: 6 residues within 4Å: Chain B: D.70, S.71, I.74, L.99, F.102, L.104 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.69 EDO.10: 8 residues within 4Å: Chain B: Y.46, K.54, P.55, K.177, I.178, L.179, G.180 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.54

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

PGE.5: 9 residues within 4Å: Chain A: G.68, S.69, D.70, S.71, I.74, D.98, L.99, F.102, L.104 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.69, A:S.71, A:S.71 PGE.6: 5 residues within 4Å: Chain A: D.117, K.120, K.121, N.124, N.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.121 Water bridges: A:N.124 PGE.12: 6 residues within 4Å: Chain A: G.165 Chain B: K.134, T.135, E.136, K.139, L.166 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:I.8, B:E.136, B:K.139, A:G.165

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.11: 9 residues within 4Å: Chain B: N.4, K.5, R.6, Y.17, L.75, T.76, D.79, H.106, D.107 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.4, B:T.76, B:T.76 Water bridges: B:R.6

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

PEG.13: 8 residues within 4Å: Chain B: V.9, 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:N.21, B:T.73

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

P-granule scaffold

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