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Ciliary neurotrophic factor

Analyse Ciliary neurotrophic factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CNT
Type: protein
Length: 552 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ciliary neurotrophic factor
UniProt: P26441
Ligands: YB, SO4
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Ciliary neurotrophic factor	protein	150	76% helix, 0% strand	P26441
2	Ciliary neurotrophic factor	protein	130	82% helix, 0% strand	P26441
3	Ciliary neurotrophic factor	protein	146	78% helix, 0% strand	P26441
4	Ciliary neurotrophic factor	protein	126	84% helix, 0% strand	P26441

Ligands and binding sites

YB · Ytterbium (III) ion · metal
SO4 · Sulfate ion · ion · 4 copies · chains 1, 3

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	407	0.70	0.82	42	empty
2	330	0.70	0.83	40	empty
3	180	0.43	0.73	27	empty
4	55	0.37	0.79	16	empty

Interfaces

3 interfaces between chains.

1–4 · 1052 Å² buried · 6 hydrogen bonds · protein-protein
2–3 · 790 Å² buried · 9 hydrogen bonds · protein-protein
1–3 · 316 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1CNT · Ciliary neurotrophic factor · the same entry in another collection · chain 4 against 4, TM-score 1.00
P26441 · AlphaFold monomer V2.0 prediction for ciliary neurotrophic factor (P26441) · a predicted model of the same protein · chain 3 against A, TM-score 0.97

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 P26441
Elsewhere: RCSB PDB 1CNT · PDBe 1CNT · UniProt P26441

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