SMTL ID : 8g9z.1 (1 other biounit)

High-resolution crystal structure of the human selenomethionine-derived SepSecS-tRNASec complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

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

PLR.1: 16 residues within 4Å: Chain A: 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, P.331, G.332, R.333 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:I.190, A:Q.192, A:A.274, A:K.304 Hydrogen bonds: A:T.164, A:T.164, A:G.165, A:Q.192, A:S.194, A:N.272, D:R.333 Salt bridges: A:K.304, D:R.95 Water bridges: D:R.95 PLR.3: 16 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 E: R.95, P.331, G.332, R.333 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:I.190, B:Q.192, B:A.274, B:K.304 Hydrogen bonds: B:T.164, B:T.164, B:G.165, B:Q.192, B:S.194, B:S.194, B:N.272, E:R.333 Water bridges: B:Y.275, B:Y.275, E:R.95 Salt bridges: B:K.304, E:R.95 PLR.5: 16 residues within 4Å: Chain A: R.95, 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 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain A 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:N.272, A:R.333 Salt bridges: D:K.304, A:R.95 Water bridges: A:R.95 PLR.7: 16 residues within 4Å: Chain B: R.95, P.331, G.332, R.333 Chain E: A.163, T.164, G.165, I.190, Q.192, S.194, C.195, S.245, N.272, A.274, Y.275, K.304 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain B 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:S.194, E:N.272, B:R.333 Water bridges: E:Y.275, B:R.95 Salt bridges: E:K.304, B:R.95

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 9 residues within 4Å: Chain A: E.49, I.52, R.53, L.56, E.77, M.81, L.133 Chain E: Y.37, G.41 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.53, A:L.56, A:L.133 Hydrogen bonds: A:E.77, A:E.77 MPD.4: 5 residues within 4Å: Chain B: I.52, R.53, L.56, E.77 Chain D: G.41 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:G.41 Hydrophobic interactions: B:I.52, B:R.53 MPD.6: 9 residues within 4Å: Chain B: Y.37, G.41 Chain D: E.49, I.52, R.53, L.56, E.77, M.81, L.133 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:R.53, D:L.56, D:L.133 Hydrogen bonds: D:E.77 MPD.8: 5 residues within 4Å: Chain A: G.41 Chain E: I.52, R.53, L.56, E.77 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.52, E:R.53 Hydrogen bonds: E:E.49, A:G.41

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

2023-04-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
A

E
B

O-phosphoseryl-tRNA(Sec) selenium transferase

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