SMTL ID : 4kzd.1 (2 other biounits)

Crystal structure of an RNA aptamer in complex with fluorophore and Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 8 residues within 4Å: Chain A: K.46, G.47, L.48, E.49, S.66 Chain B: T.98, F.99, Q.101 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.49, A:S.66, A:S.66, B:F.99, B:F.99, B:Q.101, A:K.46, A:K.46, A:G.47, A:L.48, B:Q.101, B:Q.101 Water bridges: A:W.50, A:W.50, B:Q.4, B:Q.4, B:F.99, A:L.48, A:E.49

1 x K: POTASSIUM ION(Non-functional Binders)

K.2: 8 residues within 4Å: Chain C: G.22, G.23, G.26, G.27, G.54, G.57, G.59, G.61 No protein-ligand interaction detected (PLIP)

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

MG.3: 3 residues within 4Å: Chain C: C.41, A.42, C.43 No protein-ligand interaction detected (PLIP)

1 x 1TU: 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol(Non-functional Binders)

1TU.4: 8 residues within 4Å: Chain C: G.23, G.28, U.29, U.50, A.53, G.54, A.58, G.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H. et al., A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat.Chem.Biol. (2014)

Release Date

2014-06-18

Peptides

BL3-6 Fab antibody, heavy chain: A
BL3-6 Fab antibody, light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

BL3-6 Fab antibody, heavy chain

BL3-6 Fab antibody, light chain

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