Research workbench

Interleukin-8 with an added disulfide between residues 5 and 33 (L5C/H33C)

Analyse Interleukin-8 with an added disulfide between residues 5 and 33 (L5C/H33C) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QE6
Type: protein
Length: 278 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-8 variant
UniProt: P10145
Ligands: SO4
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-8 variant	protein	68	25% helix, 25% strand	P10145
B	Interleukin-8 variant	protein	71	24% helix, 27% strand	P10145
C	Interleukin-8 variant	protein	67	25% helix, 25% strand	P10145
D	Interleukin-8 variant	protein	72	24% helix, 26% strand	P10145

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	445	0.59	0.75	51	empty
2	109	0.44	0.78	18	empty
3	66	0.31	0.75	17	empty

Interfaces

5 interfaces between chains.

C–D · 1088 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1079 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 154 Å² buried · 1 hydrogen bond · protein-protein
B–D · 53 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 35 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 11 disulfide (disulfide).

Compared structures

1QE6 · Interleukin-8 with an added disulfide between residues 5 and 33 (L5C/H33C) · the same entry in another collection · chain D against D, TM-score 1.00
P10145 · AlphaFold monomer V2.0 prediction for interleukin-8 (P10145) · a predicted model of the same protein · chain C against A, TM-score 0.96

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
Elsewhere: RCSB PDB 1QE6 · PDBe 1QE6 · UniProt P10145

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.