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LY3041658 Fab bound to CXCL8

Analyse LY3041658 Fab bound to CXCL8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WZM
Type: protein
Length: 1,001 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LY3041658 Fab heavy chain; LY3041658 Fab light chain; Interleukin-8
UniProt: P10145
Pockets: 11 · best druggability 0.58

Structure

x-ray diffraction · 5 distinct chains · 7% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LY3041658 Fab heavy chain	protein	222	5% helix, 50% strand	—
B, D	LY3041658 Fab light chain	protein	213	6% helix, 50% strand	—
C	LY3041658 Fab heavy chain	protein	224	5% helix, 49% strand	—
E	Interleukin-8	protein	64	17% helix, 27% strand	P10145
F	Interleukin-8	protein	65	17% helix, 26% strand	P10145

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains B
PG4 · Tetraethylene glycol · additive · chains C, F

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	382	0.58	0.76	44	empty
2	419	0.58	0.75	48	empty
3	126	0.51	0.81	22	empty
4	123	0.50	0.80	22	empty
5	95	0.47	0.81	20	empty

Interfaces

7 interfaces between chains.

C–D · 1890 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1874 Å² buried · 17 hydrogen bonds · protein-protein
C–F · 876 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 802 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 794 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

6WZM · LY3041658 Fab bound to CXCL8 · the same entry in another collection · chain F against F, TM-score 1.00
P10145 · AlphaFold monomer V2.0 prediction for interleukin-8 (P10145) · a predicted model of the same protein · chain E against A, TM-score 0.88

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 6WZM · PDBe 6WZM · UniProt P10145

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