SMTL ID : 5kla.1

Crystal structure of the drosophila Pumilio RNA-binding domain in complex with hunchback RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

monomer

Ligands

1 x U- G- U- A- C- A- U- A: RNA (5'-R(*UP*GP*UP*AP*CP*AP*UP*A)-3')(Non-covalent)

U-G-U-A-C-A-U-A.1: 39 residues within 4Å: Chain A: Q.34, S.37, R.38, Q.41, V.70, F.71, N.73, Y.74, Q.77, M.106, Y.107, C.109, R.110, Q.113, N.143, H.146, C.181, R.182, Q.185, R.186, Q.214, Y.215, N.217, Y.218, Q.221, K.250, F.251, S.253, N.254, E.257, Q.290, Y.291, N.293, Y.294, V.295, Q.297, Y.327, H.330 Ligands: ACT.5 Protein-ligand interaction information (PLIP) not available

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: D.132, G.133, H.134, V.135, L.136, F.162, A.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.133, A:V.135, A:L.136 EDO.3: 1 residues within 4Å: Chain A: N.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.17

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 1 residues within 4Å: Chain A: K.310 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.310 ACT.5: 3 residues within 4Å: Chain A: R.110 Ligands: U-G-U-A-C-A-U-A.1, U-G-U-A-C-A-U-A.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.110 ACT.6: 3 residues within 4Å: Chain A: H.249, K.250, F.251 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.250 Water bridges: A:K.250 Salt bridges: A:H.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weidmann, C.A. et al., Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio. Elife (2016)

Release Date

2016-08-17

Peptides

Maternal protein pumilio: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maternal protein pumilio

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