SMTL ID : 4zdp.2 (1 other biounit)

The crystal structure of Y334C mutant of human SepSecS in complex with selenocysteine tRNA (tRNASec)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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 D: R.75, S.98, P.311, G.312, R.313 15 PLIP interactions: 2 interactions with chain D, 13 interactions with chain A Hydrogen bonds: D:R.313, A:T.144, A:T.144, A:G.145, A:S.174, A:N.252 Salt bridges: D:R.75, A:K.284 Hydrophobic interactions: A:I.170, A:Q.172, A:A.254, A:K.284 Water bridges: A:M.146, A:Y.255, A:Y.255 PLR.3: 15 residues within 4Å: Chain B: A.143, T.144, G.145, I.170, Q.172, S.174, C.175, N.252, A.254, Y.255, K.284 Chain E: R.75, S.98, G.312, R.313 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:I.170, B:Q.172, B:A.254, B:K.284 Hydrogen bonds: B:T.144, B:G.145, B:S.174, B:S.174, B:N.252, E:S.98, E:R.313 Salt bridges: B:K.284, E:R.75 PLR.5: 17 residues within 4Å: Chain A: R.75, S.98, 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: 12 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:I.170, D:Q.172, D:A.254, D:K.284 Hydrogen bonds: D:T.144, D:G.145, D:S.174, D:N.252, D:K.284, A:R.313 Water bridges: D:M.146, D:Y.255 Salt bridges: D:K.284, A:R.75 PLR.7: 15 residues within 4Å: Chain B: R.75, S.98, G.312, R.313 Chain E: A.143, T.144, G.145, I.170, Q.172, S.174, C.175, N.252, A.254, Y.255, K.284 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:I.170, E:Q.172, E:A.254, E:K.284 Hydrogen bonds: E:T.144, E:G.145, E:S.174, E:S.174, E:N.252, B:S.98, B:R.313 Salt bridges: E:K.284, B:R.75

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: R.97, S.98, Q.105, R.313 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.98, A:Q.105 Water bridges: A:R.313, A:R.313 Salt bridges: A:R.97, A:R.313 PO4.4: 4 residues within 4Å: Chain B: R.97, S.98, Q.105, R.313 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.98, B:Q.105 Salt bridges: B:R.97, B:R.313 PO4.6: 4 residues within 4Å: Chain D: R.97, S.98, Q.105, R.313 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.98, D:Q.105 Water bridges: D:R.313, D:R.313 Salt bridges: D:R.97, D:R.313 PO4.8: 4 residues within 4Å: Chain E: R.97, S.98, Q.105, R.313 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.98, E:Q.105 Salt bridges: E:R.97, E:R.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Puppala, A.K. et al., Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase. Sci Rep (2016)

Release Date

2016-04-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

D
C

E
D

O-phosphoseryl-tRNA(Sec) selenium transferase

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