SMTL ID : 3w3s.1

Crystal structure of A. aeolicus tRNASec in complex with M. kandleri SerRS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: A.317, C.319, E.368, F.409, C.478 Ligands: SSA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.319, A:E.368, A:C.478 ZN.26: 6 residues within 4Å: Chain C: A.317, C.319, E.368, F.409, C.478 Ligands: SSA.27 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.319, C:E.368, C:C.478

2 x SSA: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE(Non-covalent)

SSA.2: 21 residues within 4Å: Chain A: A.317, C.319, R.349, E.351, R.360, V.361, F.364, R.366, E.368, F.409, S.449, V.450, G.451, S.452, N.454, C.478, G.482, R.485 Ligands: ZN.1, PT.3, PT.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:A.317, A:R.349, A:E.351, A:V.361, A:R.366, A:R.366, A:E.368, A:S.449, A:G.451, A:S.452, A:S.452, A:G.482, A:R.485 Salt bridges: A:R.349, A:R.366 pi-Stacking: A:F.364, A:F.364 pi-Cation interactions: A:R.485 SSA.27: 21 residues within 4Å: Chain C: A.317, C.319, R.349, E.351, R.360, V.361, F.364, R.366, E.368, F.409, S.449, V.450, G.451, S.452, N.454, C.478, G.482, R.485 Ligands: ZN.26, PT.28, PT.29 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:A.317, C:R.349, C:E.351, C:V.361, C:R.366, C:R.366, C:E.368, C:S.449, C:G.451, C:S.452, C:S.452, C:G.482, C:R.485 Salt bridges: C:R.349, C:R.366 pi-Stacking: C:F.364, C:F.364 pi-Cation interactions: C:R.485

30 x PT: PLATINUM (II) ION(Non-covalent)(Non-functional Binders)

PT.3: 3 residues within 4Å: Chain A: F.364, R.485 Ligands: SSA.2 Ligand excluded by PLIP PT.4: 3 residues within 4Å: Chain A: F.409, Y.410 Ligands: SSA.2 Ligand excluded by PLIP PT.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.6: 2 residues within 4Å: Chain A: E.75 Chain B: U.53 Ligand excluded by PLIP PT.7: 3 residues within 4Å: Chain A: R.72, H.74, D.153 Ligand excluded by PLIP PT.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.9: 3 residues within 4Å: Chain A: R.260, H.263, L.416 Ligand excluded by PLIP PT.10: 1 residues within 4Å: Chain A: E.105 Ligand excluded by PLIP PT.11: 2 residues within 4Å: Chain A: P.375, E.422 Ligand excluded by PLIP PT.12: 2 residues within 4Å: Chain A: R.193, G.194 Ligand excluded by PLIP PT.13: 3 residues within 4Å: Chain A: R.166, S.167, R.414 Ligand excluded by PLIP PT.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.15: 1 residues within 4Å: Chain A: E.144 Ligand excluded by PLIP PT.16: 2 residues within 4Å: Chain C: L.523, T.524 Ligand excluded by PLIP PT.17: 2 residues within 4Å: Chain A: E.511, K.512 Ligand excluded by PLIP PT.28: 3 residues within 4Å: Chain C: F.364, R.485 Ligands: SSA.27 Ligand excluded by PLIP PT.29: 3 residues within 4Å: Chain C: F.409, Y.410 Ligands: SSA.27 Ligand excluded by PLIP PT.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.31: 2 residues within 4Å: Chain C: E.75 Chain D: U.53 Ligand excluded by PLIP PT.32: 3 residues within 4Å: Chain C: R.72, H.74, D.153 Ligand excluded by PLIP PT.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.34: 3 residues within 4Å: Chain C: R.260, H.263, L.416 Ligand excluded by PLIP PT.35: 1 residues within 4Å: Chain C: E.105 Ligand excluded by PLIP PT.36: 2 residues within 4Å: Chain C: P.375, E.422 Ligand excluded by PLIP PT.37: 2 residues within 4Å: Chain C: R.193, G.194 Ligand excluded by PLIP PT.38: 3 residues within 4Å: Chain C: R.166, S.167, R.414 Ligand excluded by PLIP PT.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.40: 1 residues within 4Å: Chain C: E.144 Ligand excluded by PLIP PT.41: 2 residues within 4Å: Chain A: L.523, T.524 Ligand excluded by PLIP PT.42: 2 residues within 4Å: Chain C: E.511, K.512 Ligand excluded by PLIP

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.18: 2 residues within 4Å: Chain A: R.40, R.83 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: R.40, G.41 Chain B: A.64, G.65 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain A: M.1, F.110, D.111, R.112, E.164 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain A: N.296, E.297 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain A: R.308, D.309 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain A: R.308, Y.312 Chain C: R.212, W.350 Ligand excluded by PLIP SO4.24: 1 residues within 4Å: Chain B: G.52 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: C.54, C.55, C.56 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain C: R.40, R.83 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain C: R.40, G.41 Chain D: A.64, G.65 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain C: M.1, F.110, D.111, R.112, E.164 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain C: N.296, E.297 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain C: R.308, D.309 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain A: R.212, W.350 Chain C: R.308, Y.312 Ligand excluded by PLIP SO4.49: 1 residues within 4Å: Chain D: G.52 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain D: C.54, C.55, C.56 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itoh, Y. et al., Tertiary structure of bacterial selenocysteine tRNA. Nucleic Acids Res. (2013)

Release Date

2013-02-13

Peptides

Type-2 serine--tRNA ligase: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

Type-2 serine--tRNA ligase