Research workbench
Cxcr-1 N-terminal peptide bound to interleukin-8 (minimized mean)
Analyse Cxcr-1 N-terminal peptide bound to interleukin-8 (minimized mean) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ILQ
- Type
- protein
- Length
- 158 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-8 precursor; Interleukin-8 receptor a
- UniProt
- P10145, P25024
- Ligands
- ACE, ACA, NH2
- Pockets
- 2 · best druggability 0.58
Structure
solution nmr · 2 distinct chains · 22% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Interleukin-8 precursor | protein | 71 | 27% helix, 24% strand | P10145 |
| C | Interleukin-8 receptor a | protein | 16 | 0% helix, 0% strand | P25024 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, C
- ACA · 6-aminohexanoic acid · ligand · chains A, C
- NH2 · Amino group · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.58 | 0.79 | 32 | empty |
| 2 | 55 | 0.27 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 854 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 778 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
- 1ILQ · Cxcr-1 N-terminal peptide bound to interleukin-8 (minimized mean) · the same entry in another collection · chain A against A, TM-score 1.00
- P10145 · AlphaFold monomer V2.0 prediction for interleukin-8 (P10145) · a predicted model of the same protein · chain A against A, TM-score 0.86
- P25024 · AlphaFold monomer V2.0 prediction for C-X-C chemokine receptor type 1 (P25024) · a predicted model of the same protein · chain C against A, TM-score 0.17
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 P10145
- Every structure of UniProt P25024
- Elsewhere: RCSB PDB 1ILQ · PDBe 1ILQ · UniProt P10145 · UniProt P25024
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