SMTL ID : 3hl2.1 (1 other biounit)

The crystal structure of the human SepSecS-tRNASec complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 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 A: A.143, T.144, G.145, I.170, Q.172, S.174, C.175, S.225, N.252, A.254, Y.255, K.284 Chain C: E.74, R.75, P.311, G.312, R.313 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.170, A:Q.172, A:A.254, A:K.284 Hydrogen bonds: A:T.144, A:T.144, A:T.144, A:G.145, A:Q.172, A:S.174, A:S.174, A:N.252, C:R.313 Water bridges: A:Y.255, C:E.74, C:R.75, C:R.75 Salt bridges: A:K.284, C:R.75 PLR.4: 16 residues within 4Å: Chain B: A.143, T.144, G.145, I.170, Q.172, S.174, C.175, S.225, N.252, A.254, Y.255, K.284 Chain D: R.75, P.311, G.312, R.313 14 PLIP interactions: 3 interactions with chain D, 11 interactions with chain B Hydrogen bonds: D:R.313, B:T.144, B:T.144, B:T.144, B:G.145, B:Q.172, B:S.174, B:N.252 Water bridges: D:R.75 Salt bridges: D:R.75, B:K.284 Hydrophobic interactions: B:I.170, B:A.254, B:K.284 PLR.7: 17 residues within 4Å: Chain A: E.74, R.75, P.311, G.312, R.313 Chain C: A.143, T.144, G.145, I.170, Q.172, S.174, C.175, S.225, N.252, A.254, Y.255, K.284 20 PLIP interactions: 6 interactions with chain A, 14 interactions with chain C Hydrogen bonds: A:E.74, A:R.313, C:T.144, C:T.144, C:G.145, C:Q.172, C:S.174, C:S.174, C:N.252, C:K.284 Water bridges: A:E.74, A:R.75, A:R.75, C:Y.255 Salt bridges: A:R.75, C:K.284 Hydrophobic interactions: C:I.170, C:Q.172, C:A.254, C:K.284 PLR.10: 16 residues within 4Å: Chain B: R.75, P.311, G.312, R.313 Chain D: A.143, T.144, G.145, I.170, Q.172, S.174, C.175, S.225, N.252, A.254, Y.255, K.284 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:I.170, D:A.254, D:K.284 Hydrogen bonds: D:T.144, D:T.144, D:G.145, D:Q.172, D:S.174, D:N.252, B:E.74, B:R.313 Salt bridges: D:K.284, B:R.75 Water bridges: B:R.75

4 x TS6: Monothiophosphate(Non-covalent)

TS6.2: 4 residues within 4Å: Chain A: R.97, S.98, Q.105, R.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.98, A:Q.105 Water bridges: A:R.313, A:R.313 TS6.3: 2 residues within 4Å: Chain A: R.199, H.368 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.199, A:R.199, A:H.368 TS6.8: 4 residues within 4Å: Chain C: R.97, S.98, Q.105, R.313 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.98, C:Q.105 Water bridges: C:R.313, C:R.313 TS6.9: 2 residues within 4Å: Chain C: R.199, H.368 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.199, C:R.199, C:H.368

4 x SEP: PHOSPHOSERINE(Non-functional Binders)

SEP.5: 5 residues within 4Å: Chain B: R.97, S.98, G.99, Q.105 Chain D: K.173 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.97, B:S.98, B:G.99, B:Q.105, B:Q.105 Salt bridges: B:R.97, B:R.97, D:K.173 SEP.6: 3 residues within 4Å: Chain B: R.199, R.234, H.368 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.234 Salt bridges: B:R.199, B:H.368, B:H.368 SEP.11: 5 residues within 4Å: Chain B: K.173 Chain D: R.97, S.98, G.99, Q.105 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.97, D:S.98, D:G.99, D:Q.105, D:Q.105 Salt bridges: D:R.97, D:R.97, B:K.173 SEP.12: 3 residues within 4Å: Chain D: R.199, R.234, H.368 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.234 Salt bridges: D:R.199, D:H.368, D:H.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palioura, S. et al., The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation. Science (2009)

Release Date

2009-10-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

O-phosphoseryl-tRNA(Sec) selenium transferase

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