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Crystal structure of apc-arm in complexed with AMER1-A2

Analyse Crystal structure of apc-arm in complexed with AMER1-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YJL
Type: protein
Length: 2,107 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenomatous polyposis COLI protein; Apc membrane recruitment protein 1
UniProt: P25054, Q5JTC6
Pockets: 15 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenomatous polyposis COLI protein	protein	337	73% helix, 0% strand	P25054
B	Adenomatous polyposis COLI protein	protein	337	73% helix, 0% strand	P25054
C	Adenomatous polyposis COLI protein	protein	338	72% helix, 0% strand	P25054
D, E, F	Adenomatous polyposis COLI protein	protein	339	72% helix, 0% strand	P25054
G, H, I, J, K, L	Apc membrane recruitment protein 1	protein	13	0% helix, 0% strand	Q5JTC6

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 37 copies · chains A, E, F, D, B, C

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1078	0.76	0.78	89	EDO
2	1165	0.75	0.78	93	EDO
3	1048	0.75	0.77	85	EDO
4	1146	0.75	0.77	105	EDO
5	179	0.51	0.77	27	empty

Interfaces

15 interfaces between chains.

D–I · 1096 Å² buried · 26 hydrogen bonds · protein-protein
F–L · 1094 Å² buried · 26 hydrogen bonds · protein-protein
C–H · 1093 Å² buried · 26 hydrogen bonds · protein-protein
E–J · 1086 Å² buried · 28 hydrogen bonds · protein-protein
B–K · 1071 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

4YJL · Crystal structure of APC-ARM in complexed with Amer1-A2 · the same entry in another collection · chain L against L, TM-score 1.00

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 P25054
Every structure of UniProt Q5JTC6
Elsewhere: RCSB PDB 4YJL · PDBe 4YJL · UniProt P25054 · UniProt Q5JTC6

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