MolNFT v1 · #60986 · protein

Crystal structure of il-23 in complex with neutralizing Fab

3D85 · Fab of antibody 7G10, light chain: “Crystal structure of il-23 in complex with neutralizing Fab”. X-ray diffraction, 9 pockets (best druggability 0.67). MolNFT v1 #60986 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3D85
Type: protein
Length: 852 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab of antibody 7G10, light chain; Fab of antibody 7G10, heavy chain; Interleukin-23…
UniProt: Q9NPF7, P29460
Pockets: 9 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab of antibody 7G10, light chain	protein	213	7% helix, 51% strand	—
B	Fab of antibody 7G10, heavy chain	protein	216	10% helix, 50% strand	—
C	Interleukin-23 subunit P19	protein	133	71% helix, 0% strand	Q9NPF7
D	Interleukin-12 subunit P40	protein	290	2% helix, 54% strand	P29460

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C
IMD · Imidazole · additive · chains A

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	762	0.67	0.75	60	empty
2	128	0.61	0.86	28	empty
3	50	0.55	0.90	18	empty
4	229	0.54	0.77	33	empty
5	142	0.52	0.80	23	empty

Interfaces

4 interfaces between chains.

A–B · 1731 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 933 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 496 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 362 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

3D85 · Crystal structure of IL-23 in complex with neutralizing FAB · the same entry in another collection · chain D against D, TM-score 1.00
P29460 · AlphaFold monomer V2.0 prediction for interleukin-12 subunit beta (P29460) · a predicted model of the same protein · chain D against A, TM-score 0.96
Q9NPF7 · AlphaFold monomer V2.0 prediction for interleukin-23 subunit alpha (Q9NPF7) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 Q9NPF7
Every structure of UniProt P29460
Elsewhere: RCSB PDB 3D85 · PDBe 3D85 · UniProt Q9NPF7 · UniProt P29460

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