SMTL ID : 3u4m.1

Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: E.198, K.201, T.208, F.209, L.210, H.228 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.198, A:F.209, A:L.210 Salt bridges: A:K.201, A:H.228 SO4.12: 3 residues within 4Å: Chain B: C.71, A.72 Ligands: MG.19 No protein-ligand interaction detected (PLIP)

7 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 8 residues within 4Å: Chain A: A.34, A.36, F.38, D.39, E.40, A.179, S.180 Ligands: MG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.39, A:E.40, A:E.40 MLI.3: 6 residues within 4Å: Chain A: A.113, T.145, I.157, R.161, I.162, E.163 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.163 Hydrogen bonds: A:R.161, A:E.163 Salt bridges: A:R.161 MLI.4: 2 residues within 4Å: Chain A: F.38, D.39 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.39 Hydrogen bonds: A:D.39, A:D.39 MLI.13: 5 residues within 4Å: Chain B: A.30, A.31, G.52, G.53, A.54 No protein-ligand interaction detected (PLIP) MLI.14: 2 residues within 4Å: Chain B: C.74, C.75 No protein-ligand interaction detected (PLIP) MLI.15: 3 residues within 4Å: Chain B: U.26, G.27, G.55 No protein-ligand interaction detected (PLIP) MLI.16: 5 residues within 4Å: Chain B: A.15, G.17, U.18, A.66, A.67 No protein-ligand interaction detected (PLIP)

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 6 residues within 4Å: Chain A: A.34, T.35, A.36, F.38, E.40 Ligands: MLI.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.34, A:A.36, A:F.38, A:E.40 MG.17: 3 residues within 4Å: Chain B: U.18, G.19 Ligands: MG.18 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: MG.17 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain B: G.16 Ligands: SO4.12 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain B: U.68 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: G.81, E.82 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: G.61, T.62, H.200 Ligand excluded by PLIP

5 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: R.7, A.10, L.11, T.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.35, A:T.35 NA.9: 10 residues within 4Å: Chain A: R.7, L.11, L.33, A.34, T.35, A.36, E.40, T.217, M.219, G.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.7, A:T.35, A:A.36, A:E.40, A:T.217 NA.10: 4 residues within 4Å: Chain A: K.6, R.7 Chain B: C.25, U.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.7 Water bridges: A:G.5, A:R.7 NA.11: 7 residues within 4Å: Chain A: E.43, T.216, T.217, T.218 Chain B: G.19, C.71, A.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.216 NA.21: 5 residues within 4Å: Chain A: E.43, H.45, H.173 Chain B: G.19, G.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tishchenko, S. et al., High-resolution crystal structure of the isolated ribosomal L1 stalk. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-08-08

Peptides

50S ribosomal protein L1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

50S ribosomal protein L1

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