SMTL ID : 4zdl.1

The crystal structure of the T325S mutant of the human holo SepSecS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 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, N.252, A.254, Y.255, K.284 Chain C: R.75, S.98, P.311, G.312, R.313 Ligands: FLC.2 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.170, A:Q.172, A:A.254, A:K.284 Hydrogen bonds: A:T.144, A:G.145, A:Q.172, A:S.174, A:N.252, C:S.98, C:S.98, C:R.313 Water bridges: A:M.146, A:Y.255, A:Y.255 Salt bridges: A:K.284, C:R.75 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 D: R.75, P.311, G.312, R.313 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:I.170, B:Q.172, B:A.254, B:K.284 Hydrogen bonds: B:T.144, B:T.144, B:G.145, B:Q.172, B:S.174, B:N.252, B:K.284, D:R.313 Salt bridges: B:K.284, D:R.75 Water bridges: D:R.75, D:R.75 PLR.4: 17 residues within 4Å: Chain A: R.75, S.98, P.311, G.312, R.313 Chain C: A.143, T.144, G.145, I.170, Q.172, S.174, C.175, N.252, A.254, Y.255, K.284 Ligands: FLC.5 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:I.170, C:Q.172, C:A.254, C:K.284 Hydrogen bonds: C:T.144, C:G.145, C:Q.172, C:S.174, C:N.252, A:S.98, A:S.98, A:R.313 Water bridges: C:M.146, C:Y.255, A:E.74 Salt bridges: C:K.284, A:R.75 PLR.6: 15 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, N.252, A.254, Y.255, K.284 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:I.170, D:Q.172, 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, D:K.284, B:R.313 Salt bridges: D:K.284, B:R.75 Water bridges: B:R.75, B:R.75

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 8 residues within 4Å: Chain C: R.75, R.97, S.98, G.99, Q.105, K.107, R.313 Ligands: PLR.1 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:E.74, C:R.97, C:S.98, C:S.98, C:G.99, C:Q.105, C:R.313 Salt bridges: C:R.75, C:R.97, C:K.107, C:R.313, A:K.173, A:K.284 Water bridges: A:Q.172 FLC.5: 8 residues within 4Å: Chain A: R.75, R.97, S.98, G.99, Q.105, K.107, R.313 Ligands: PLR.4 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:E.74, A:R.97, A:S.98, A:S.98, A:G.99, A:Q.105, A:R.313 Salt bridges: A:R.75, A:R.97, A:K.107, A:R.313, C:K.173, C:K.284 Water bridges: C:Q.172

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: 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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