› 4ni7

X-ray diffraction
2.4Å resolution

Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025)

Released:
DOI: 10.2210/pdb4ni7/pdb
PDB entry 4ni7 coloured by chain, front view.
PDB entry 4ni7 coloured by chain, side view.
PDB entry 4ni7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of interleukin-6 in complex with a modified nucleic acid ligand.
Gelinas AD, Davies DR, Edwards TE, Rohloff JC, Carter JD, Zhang C, Gupta S, Ishikawa Y, Hirota M, Nakaishi Y, Jarvis TC, Janjic N
J Biol Chem 289 8720-34 (2014)
PMID: 24415767

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117871 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Interleukin-6 Chain: A
Molecule details ›
Chain: A
Length: 186 amino acids
Theoretical weight: 21.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P05231 (Residues: 28-212; Coverage: 100%)
Gene names: IFNB2, IL6
Sequence domains: Interleukin-6/G-CSF/MGF family
Structure domains: Growth Hormone; Chain: A;
SOMAmer SL1025 Chain: B
Molecule details ›
Chain: B
Length: 32 nucleotides
Theoretical weight: 11.4 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 2 x NA
5 modified residues:
Ligand OMC 3 x OMC
Ligand OMG 1 x OMG
Ligand DUZ 8 x DUZ
Ligand UPE 1 x UPE
Ligand A2M 2 x A2M

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P32
Unit cell:
a: 50.23Å b: 50.23Å c: 103.63Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.222 0.26
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents.
Rohloff et al. (2014)
12 more

10 mentions without citation

Structural Biology for the Molecular Insight between Aptamers and Target Proteins.
Zhang et al. (2021)
9 more