SMTL ID : 4r3i.1

The crystal structure of an RNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: 23 residues within 4Å: Chain A: K.18, S.19, N.20, N.24, W.34, S.35, L.37, P.38, V.39, N.40, R.61, E.62, W.85, G.90, M.91, M.95, K.129, I.130, G.131, R.132, D.133 Ligands: UNX.5, UNX.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.19, A:N.20, A:N.20, A:N.24, A:S.35 Water bridges: A:N.20, A:T.36

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

UNX.2: 5 residues within 4Å: Chain A: T.119, P.121, E.138, E.140, C.141 No protein-ligand interaction detected (PLIP) UNX.3: 3 residues within 4Å: Chain A: V.25, K.29, Q.67 No protein-ligand interaction detected (PLIP) UNX.4: 6 residues within 4Å: Chain A: T.36, E.41, M.95, L.96, G.97, G.98 No protein-ligand interaction detected (PLIP) UNX.5: 2 residues within 4Å: Chain A: K.126 Ligands: G-G-6MZ-C-U.1 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: H.22, S.63 No protein-ligand interaction detected (PLIP) UNX.7: 1 residues within 4Å: Chain A: K.114 No protein-ligand interaction detected (PLIP) UNX.8: 6 residues within 4Å: Chain A: L.16, K.18, K.129, G.131 Ligands: G-G-6MZ-C-U.1, G-G-6MZ-C-U.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, C. et al., Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain. Nat.Chem.Biol. (2014)

Release Date

2014-09-17

Peptides

YTH domain-containing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YTH domain-containing protein 1

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