SMTL ID : 4rcj.1

Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x G- G- 6MZ- C- U: RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')(Non-covalent)

G-G-6MZ-C-U.1: 18 residues within 4Å: Chain A: K.32, S.33, Y.34, D.38, W.48, C.49, V.77, N.78, G.79, W.102, K.106, W.107, T.140, N.141, S.142, R.143, D.144 Ligands: UNX.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.33, A:Y.34, A:C.49, A:N.78 Water bridges: A:R.143 Salt bridges: A:K.106 pi-Stacking: A:Y.34, A:W.107, A:W.107, A:W.107

7 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 5 residues within 4Å: Chain A: L.8, H.12, I.43, K.44, S.46 No protein-ligand interaction detected (PLIP) UNX.3: 2 residues within 4Å: Chain A: N.141 Ligands: G-G-6MZ-C-U.1 No protein-ligand interaction detected (PLIP) UNX.4: 4 residues within 4Å: Chain A: S.13, Q.114, W.115, I.116 No protein-ligand interaction detected (PLIP) UNX.5: 4 residues within 4Å: Chain A: G.81, P.122, N.123, N.124 No protein-ligand interaction detected (PLIP) UNX.6: 3 residues within 4Å: Chain A: P.122, N.124, Q.125 No protein-ligand interaction detected (PLIP) UNX.7: 4 residues within 4Å: Chain A: H.128, I.129, R.130, K.152 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain A: H.175, Y.176, R.179 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, C. et al., Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. J.Biol.Chem. (2015)

Release Date

2014-11-12

Peptides

YTH domain-containing family protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing family protein 1