Research workbench

Crystal structure of APC11 ring domain

Analyse Crystal structure of APC11 ring domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R2Y
Type: protein
Length: 250 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anaphase-promoting complex subunit 11
UniProt: Q9NYG5
Ligands: ZN
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 4 distinct chains · 19% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anaphase-promoting complex subunit 11	protein	64	22% helix, 19% strand	Q9NYG5
B	Anaphase-promoting complex subunit 11	protein	59	19% helix, 20% strand	Q9NYG5
C	Anaphase-promoting complex subunit 11	protein	65	17% helix, 18% strand	Q9NYG5
D	Anaphase-promoting complex subunit 11	protein	62	18% helix, 19% strand	Q9NYG5

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, C, D

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

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	191	0.54	0.78	27	empty
2	114	0.48	0.80	22	empty
3	52	0.25	0.72	12	empty

Interfaces

5 interfaces between chains.

A–B · 1411 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1410 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 459 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 23 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 15 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4R2Y · Crystal structure of APC11 RING domain · the same entry in another collection · chain C against C, TM-score 1.00
Q9NYG5 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 11 (Q9NYG5) · a predicted model of the same protein · chain B against A, TM-score 0.69

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 Q9NYG5
Elsewhere: RCSB PDB 4R2Y · PDBe 4R2Y · UniProt Q9NYG5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.