Research workbench
Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (somamer SL1025), form 2
Analyse Crystal structure of human interleukin 6 in complex with a modified nucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NI9
- Type
- protein + DNA
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Somamer SL1025; Interleukin-6
- UniProt
- P05231
- Ligands
- NA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Somamer SL1025 | dna | 32 | — | — |
| A | Interleukin-6 | protein | 144 | 72% helix, 0% strand | P05231 |
| C | Interleukin-6 | protein | 148 | 70% helix, 0% strand | P05231 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.82 | 0.84 | 66 | empty |
| 2 | 127 | 0.53 | 0.82 | 17 | empty |
| 3 | 99 | 0.50 | 0.82 | 18 | empty |
| 4 | 119 | 0.49 | 0.80 | 16 | empty |
| 5 | 129 | 0.36 | 0.73 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–A · 1169 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–D · 1042 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 221 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 220 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–C · 176 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 2 disulfide (nucleotide modification, disulfide).
Compared structures
- 4NI9 · Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer… · the same entry in another collection · chain B against B, TM-score 1.00
- P05231 · AlphaFold monomer V2.0 prediction for interleukin-6 (P05231) · a predicted model of the same protein · chain C against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05231
- Elsewhere: RCSB PDB 4NI9 · PDBe 4NI9 · UniProt P05231
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