MolNFT v1 · #72926 · protein

Crystal structure of apc complexed with asef

3NMX · Apc variant protein: “Crystal structure of apc complexed with asef”. X-ray diffraction, 6 pockets (best druggability 0.80). MolNFT v1 #72926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NMX
Type: protein
Length: 1,013 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apc variant protein; Rho guanine nucleotide exchange factor 4
UniProt: Q4LE70, Q9NR80
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apc variant protein	protein	326	75% helix, 0% strand	Q4LE70
B	Apc variant protein	protein	325	75% helix, 0% strand	Q4LE70
C	Apc variant protein	protein	323	74% helix, 0% strand	Q4LE70
D, E, F	Rho guanine nucleotide exchange factor 4	protein	13	31% helix, 0% strand	Q9NR80

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.80	0.82	101	empty
2	601	0.68	0.77	53	empty
3	440	0.66	0.79	45	empty
4	62	0.53	0.87	14	empty
5	202	0.50	0.76	23	empty

Interfaces

9 interfaces between chains.

A–C · 770 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 769 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 763 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 731 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 423 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3NMX · Crystal structure of APC complexed with Asef · the same entry in another collection · chain F against F, TM-score 1.00
Q9NR80 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 4 (Q9NR80) · a predicted model of the same protein · chain D against A, TM-score 0.35

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 Q4LE70
Every structure of UniProt Q9NR80
Elsewhere: RCSB PDB 3NMX · PDBe 3NMX · UniProt Q4LE70 · UniProt Q9NR80

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