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Structure of dcc FN456 domains

Analyse Structure of dcc FN456 domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X83
Type: protein
Length: 586 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Netrin receptor dcc
UniProt: P43146
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Netrin receptor dcc	protein	94	0% helix, 51% strand	P43146
B	Netrin receptor dcc	protein	202	3% helix, 48% strand	P43146
C	Netrin receptor dcc	protein	95	0% helix, 51% strand	P43146
D	Netrin receptor dcc	protein	195	4% helix, 48% strand	P43146

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	315	0.56	0.76	43	empty
2	103	0.36	0.74	23	empty
3	87	0.36	0.76	20	empty

Interfaces

4 interfaces between chains.

B–D · 882 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 431 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 425 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 116 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5X83 · Structure of DCC FN456 domains · the same entry in another collection · chain D against D, TM-score 1.00
P43146 · AlphaFold monomer V2.0 prediction for netrin receptor dcc (P43146) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P43146
Elsewhere: RCSB PDB 5X83 · PDBe 5X83 · UniProt P43146

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