SMTL ID : 3egz.1

Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 3 residues within 4Å: Ligands: MG.14, MG.27, MG.40 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain B: G.9 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: G.7, A.8, A.53 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: G.15 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: A.13, G.15 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: U.11 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: A.54, A.55 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain B: C.57 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain B: U.37 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: A.29, G.30 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain B: G.21 Ligands: CTC.2 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Ligands: MG.1, MG.27, MG.40 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain D: G.9 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain D: G.7, A.8, A.53 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain D: G.15 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain D: A.13, G.15 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain D: U.11 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain D: A.54, A.55 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain D: C.57 No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain D: U.37 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain D: A.29, G.30 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain D: G.21 Ligands: CTC.15 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Ligands: MG.1, MG.14, MG.40 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain F: G.9 No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain F: G.7, A.8, A.53 No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Chain F: G.15 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain F: A.13, G.15 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Chain F: U.11 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain F: A.54, A.55 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain F: C.57 No protein-ligand interaction detected (PLIP) MG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain F: U.37 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain F: A.29, G.30 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain F: G.21 Ligands: CTC.28 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Ligands: MG.1, MG.14, MG.27 No protein-ligand interaction detected (PLIP) MG.42: 1 residues within 4Å: Chain H: G.9 No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain H: G.7, A.8, A.53 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Chain H: G.15 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain H: A.13, G.15 No protein-ligand interaction detected (PLIP) MG.46: 1 residues within 4Å: Chain H: U.11 No protein-ligand interaction detected (PLIP) MG.47: 2 residues within 4Å: Chain H: A.54, A.55 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain H: C.57 No protein-ligand interaction detected (PLIP) MG.49: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Chain H: U.37 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain H: A.29, G.30 No protein-ligand interaction detected (PLIP) MG.52: 2 residues within 4Å: Chain H: G.21 Ligands: CTC.41 No protein-ligand interaction detected (PLIP)

4 x CTC: 7-CHLOROTETRACYCLINE(Non-functional Binders)

CTC.2: 10 residues within 4Å: Chain B: G.7, A.14, G.15, U.18, G.21, A.22, U.59, A.60, C.61 Ligands: MG.13 No protein-ligand interaction detected (PLIP) CTC.15: 10 residues within 4Å: Chain D: G.7, A.14, G.15, U.18, G.21, A.22, U.59, A.60, C.61 Ligands: MG.26 No protein-ligand interaction detected (PLIP) CTC.28: 10 residues within 4Å: Chain F: G.7, A.14, G.15, U.18, G.21, A.22, U.59, A.60, C.61 Ligands: MG.39 No protein-ligand interaction detected (PLIP) CTC.41: 10 residues within 4Å: Chain H: G.7, A.14, G.15, U.18, G.21, A.22, U.59, A.60, C.61 Ligands: MG.52 No protein-ligand interaction detected (PLIP)

Links

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Citation

Xiao, H. et al., Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. Chem.Biol. (2008)

Release Date

2008-10-28

Peptides

U1 small nuclear ribonucleoprotein A: ACEG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

U1 small nuclear ribonucleoprotein A

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