SMTL ID : 5uc6.1

Structural insights into IL-1 alpha recognition by a naphthyl-modified aptamer that mimics IL-1RI Domain III

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.11, Y.12, N.13, K.60, S.61, S.62 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.11 MG.3: 6 residues within 4Å: Chain A: Y.121, F.122, F.131, I.132, T.150, F.152 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.132, A:T.150 MG.4: 6 residues within 4Å: Chain A: Y.39, L.40, P.89, V.90, W.139, V.140 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.90, A:V.140 MG.5: 7 residues within 4Å: Chain A: A.83, T.107, N.108, L.110, F.111, S.124, V.125 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.108, A:L.110, A:S.124

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: D.64, D.65 Chain B: X.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.64

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 1 residues within 4Å: Chain B: G.22 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, X. et al., Structural basis for IL-1 alpha recognition by a modified DNA aptamer that specifically inhibits IL-1 alpha signaling. Nat Commun (2017)

Release Date

2017-10-11

Peptides

Interleukin-1 alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Interleukin-1 alpha