SMTL ID : 7mdl.1 (1 other biounit)

High-resolution crystal structure of human SepSecS-tRNASec complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-tetramer

Ligands

4 x PLR: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE(Covalent)

PLR.1: 17 residues within 4Å: Chain B: A.163, T.164, G.165, I.190, Q.192, S.194, C.195, S.245, N.272, A.274, Y.275, K.304 Chain D: R.95, S.118, P.331, G.332, R.333 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:I.190, B:Q.192, B:A.274, B:K.304 Hydrogen bonds: B:T.164, B:G.165, B:Q.192, B:S.194, B:S.194, B:N.272, D:R.333 Water bridges: B:Y.275 Salt bridges: B:K.304, D:R.95 PLR.3: 16 residues within 4Å: Chain C: A.163, T.164, G.165, I.190, Q.192, S.194, C.195, N.272, A.274, Y.275, K.304 Chain E: R.95, S.118, P.331, G.332, R.333 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:I.190, C:Q.192, C:A.274, C:K.304 Hydrogen bonds: C:T.164, C:G.165, C:Q.192, C:S.194, C:N.272, E:R.333 Water bridges: C:Y.275 Salt bridges: E:R.95 PLR.5: 17 residues within 4Å: Chain B: R.95, S.118, P.331, G.332, R.333 Chain D: A.163, T.164, G.165, I.190, Q.192, S.194, C.195, S.245, N.272, A.274, Y.275, K.304 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.190, D:Q.192, D:A.274, D:K.304 Hydrogen bonds: D:T.164, D:G.165, D:Q.192, D:S.194, D:S.194, D:N.272, D:K.304, B:R.333 Water bridges: D:Y.275, D:Y.275 Salt bridges: D:K.304, B:R.95 PLR.7: 16 residues within 4Å: Chain C: R.95, S.118, P.331, G.332, R.333 Chain E: A.163, T.164, G.165, I.190, Q.192, S.194, C.195, N.272, A.274, Y.275, K.304 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:I.190, E:Q.192, E:A.274, E:K.304 Hydrogen bonds: E:T.164, E:G.165, E:Q.192, E:S.194, E:N.272, E:K.304, C:R.333 Water bridges: E:Y.275, E:Y.275 Salt bridges: C:R.95

4 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 6 residues within 4Å: Chain B: R.117, S.118, G.119, Q.125, R.333 Chain D: K.193 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:R.117 Hydrogen bonds: B:R.117, B:S.118, B:G.119, B:Q.125 Water bridges: B:D.120, D:Q.192, D:Q.192 Salt bridges: B:R.95, B:R.117, B:R.333, D:K.193 FLC.4: 6 residues within 4Å: Chain C: R.95, R.117, S.118, G.119, Q.125, R.333 14 PLIP interactions: 3 interactions with chain E, 11 interactions with chain C Water bridges: E:Q.192, E:Q.192, C:R.117, C:R.117 Salt bridges: E:K.193, C:R.95, C:R.117, C:R.333 Hydrophobic interactions: C:R.117 Hydrogen bonds: C:S.118, C:S.118, C:G.119, C:Q.125, C:R.333 FLC.6: 6 residues within 4Å: Chain B: K.193 Chain D: R.117, S.118, G.119, Q.125, R.333 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain D Water bridges: B:Q.192, B:Q.192, D:D.120 Salt bridges: B:K.193, D:R.95, D:R.117, D:R.333 Hydrophobic interactions: D:R.117 Hydrogen bonds: D:R.117, D:S.118, D:G.119, D:Q.125 FLC.8: 6 residues within 4Å: Chain E: R.95, R.117, S.118, G.119, Q.125, R.333 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:R.117 Hydrogen bonds: E:S.118, E:S.118, E:G.119, E:Q.125, E:R.333 Water bridges: E:R.117, E:R.117, C:Q.192, C:Q.192 Salt bridges: E:R.95, E:R.117, E:R.333, C:K.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Puppala, A.K. et al., Structural basis for the tRNA-dependent activation of the terminal complex of selenocysteine synthesis in humans. Nucleic Acids Res. (2023)

Release Date

2022-11-09

Peptides

O-phosphoseryl-tRNA(Sec) selenium transferase: BCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
A

E
B

O-phosphoseryl-tRNA(Sec) selenium transferase

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