SMTL ID : 4lck.1 (1 other biounit)

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

45 x SR: STRONTIUM ION(Non-functional Binders)

SR.1: 1 residues within 4Å: Chain B: G.68 Ligand excluded by PLIP SR.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SR.3: 1 residues within 4Å: Chain B: U.50 Ligand excluded by PLIP SR.4: 2 residues within 4Å: Chain B: G.65 Ligands: SR.14 Ligand excluded by PLIP SR.5: 1 residues within 4Å: Chain B: U.15 Ligand excluded by PLIP SR.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SR.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SR.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SR.9: 2 residues within 4Å: Chain B: G.3, G.44 Ligand excluded by PLIP SR.10: 1 residues within 4Å: Chain B: G.1 Ligand excluded by PLIP SR.11: 1 residues within 4Å: Chain B: G.40 Ligand excluded by PLIP SR.12: 2 residues within 4Å: Chain B: A.33, G.34 Ligand excluded by PLIP SR.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SR.14: 1 residues within 4Å: Ligands: SR.4 Ligand excluded by PLIP SR.15: 2 residues within 4Å: Chain B: C.58, G.59 Ligand excluded by PLIP SR.16: 3 residues within 4Å: Chain B: A.16, G.41, C.43 Ligand excluded by PLIP SR.17: 2 residues within 4Å: Chain B: G.46, G.47 Ligand excluded by PLIP SR.18: 2 residues within 4Å: Chain B: C.58, G.59 Ligand excluded by PLIP SR.19: 2 residues within 4Å: Chain B: U.27, U.28 Ligand excluded by PLIP SR.20: 2 residues within 4Å: Chain B: G.39, G.40 Ligand excluded by PLIP SR.21: 1 residues within 4Å: Chain B: G.59 Ligand excluded by PLIP SR.22: 2 residues within 4Å: Chain B: A.5, G.6 Ligand excluded by PLIP SR.23: 2 residues within 4Å: Chain B: C.23, G.38 Ligand excluded by PLIP SR.24: 1 residues within 4Å: Chain C: G.59 Ligand excluded by PLIP SR.25: 1 residues within 4Å: Chain C: G.97 Ligand excluded by PLIP SR.26: 2 residues within 4Å: Chain C: A.11, G.12 Ligand excluded by PLIP SR.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SR.28: 2 residues within 4Å: Chain C: U.55, G.59 Ligand excluded by PLIP SR.29: 1 residues within 4Å: Chain C: G.18 Ligand excluded by PLIP SR.30: 1 residues within 4Å: Chain C: U.23 Ligand excluded by PLIP SR.31: 1 residues within 4Å: Chain C: A.46 Ligand excluded by PLIP SR.32: 1 residues within 4Å: Chain C: G.67 Ligand excluded by PLIP SR.33: 2 residues within 4Å: Chain C: G.28, U.30 Ligand excluded by PLIP SR.34: 1 residues within 4Å: Chain C: C.102 Ligand excluded by PLIP SR.35: 1 residues within 4Å: Chain C: C.6 Ligand excluded by PLIP SR.36: 2 residues within 4Å: Chain C: A.42, G.43 Ligand excluded by PLIP SR.37: 1 residues within 4Å: Chain C: G.43 Ligand excluded by PLIP SR.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SR.39: 3 residues within 4Å: Chain C: U.37, G.38, G.70 Ligand excluded by PLIP SR.40: 2 residues within 4Å: Chain C: G.74, U.75 Ligand excluded by PLIP SR.41: 2 residues within 4Å: Chain C: U.4, G.5 Ligand excluded by PLIP SR.42: 1 residues within 4Å: Chain C: G.2 Ligand excluded by PLIP SR.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SR.44: 1 residues within 4Å: Chain C: A.26 Ligand excluded by PLIP SR.45: 1 residues within 4Å: Chain C: A.54 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.47: 1 residues within 4Å: Chain C: G.20 No protein-ligand interaction detected (PLIP) MG.48: 2 residues within 4Å: Chain C: G.28, A.29 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature (2013)

Release Date

2013-07-31

Peptides

Ribosomal protein YbxF: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribosomal protein YbxF

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