MolNFT v1 · #117333 · protein

Crystal structure of chicken CNTN1 FN1-FN3 domains

5E53 · Contactin-1: “Crystal structure of chicken CNTN1 FN1-FN3 domains”. X-ray diffraction, 9 pockets (best druggability 0.70). MolNFT v1 #117333 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5E53
Type: protein
Length: 1,177 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Contactin-1
UniProt: P14781
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Contactin-1	protein	288	2% helix, 44% strand	P14781
B	Contactin-1	protein	296	2% helix, 44% strand	P14781
C	Contactin-1	protein	292	2% helix, 43% strand	P14781
D	Contactin-1	protein	301	2% helix, 45% strand	P14781

Ligands and binding sites

IMD · Imidazole · additive · 15 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	432	0.70	0.81	52	empty
2	363	0.65	0.79	44	IMD
3	383	0.55	0.74	32	empty
4	95	0.38	0.76	18	empty
5	70	0.35	0.77	19	empty

Interfaces

3 interfaces between chains.

B–D · 668 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 636 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 555 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5E53 · Crystal structure of chicken CNTN1 FN1-FN3 domains · the same entry in another collection · chain D against D, TM-score 1.00
P14781 · AlphaFold monomer V2.0 prediction for contactin-1 (P14781) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 P14781
Elsewhere: RCSB PDB 5E53 · PDBe 5E53 · UniProt P14781

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