MolNFT v1 · #87085 · protein

Crystal structure of the FN5 and FN6 domains of NEO1, form 2

4BQB · Neogenin: “Crystal structure of the FN5 and FN6 domains of NEO1, form 2”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.68). MolNFT v1 #87085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4BQB
Type: protein
Length: 792 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neogenin
UniProt: P97798
Ligands: NAG
Pockets: 10 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neogenin	protein	195	2% helix, 52% strand	P97798
B	Neogenin	protein	195	2% helix, 52% strand	P97798
C	Neogenin	protein	199	2% helix, 51% strand	P97798
D	Neogenin	protein	203	1% helix, 50% strand	P97798

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

10 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	879	0.68	0.74	89	empty
2	625	0.68	0.77	77	empty
3	170	0.47	0.76	26	empty
4	109	0.46	0.79	21	empty
5	118	0.45	0.78	20	empty

Interfaces

4 interfaces between chains.

A–C · 926 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 634 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 448 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 394 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan (N-glycosylation).

Compared structures

4BQB · Crystal structure of the FN5 and FN6 domains of NEO1, form 2 · the same entry in another collection · chain D against D, TM-score 1.00
P97798 · AlphaFold monomer V2.0 prediction for neogenin (P97798) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 P97798
Elsewhere: RCSB PDB 4BQB · PDBe 4BQB · UniProt P97798

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