MolNFT v1 · #140631 · protein

The structure of DRFAM20C1 and HFAM20A complex

5YH2 · Pseudokinase FAM20A: “The structure of DRFAM20C1 and HFAM20A complex”. X-ray diffraction, 1 ligand (ATP), 20 pockets (best druggability 0.84). MolNFT v1 #140631 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YH2
Type: protein
Length: 1,645 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pseudokinase FAM20A; Family with sequence similarity 20, member ca
UniProt: Q96MK3, E7FBB8
Ligands: ATP
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pseudokinase FAM20A	protein	428	39% helix, 14% strand	Q96MK3
C	Family with sequence similarity 20, member ca	protein	395	32% helix, 12% strand	E7FBB8
B	Pseudokinase FAM20A	protein	428	39% helix, 13% strand	Q96MK3
D	Family with sequence similarity 20, member ca	protein	394	31% helix, 12% strand	E7FBB8

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D, C, B

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1140	0.84	0.85	132	ATP
2	682	0.79	0.84	70	ATP
3	638	0.75	0.81	73	empty
4	388	0.75	0.86	58	empty
5	421	0.74	0.84	57	empty

Interfaces

5 interfaces between chains.

A–C · 1075 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1052 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 852 Å² buried · 4 hydrogen bonds · protein-protein
C–B · 820 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 88 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

5YH2 · The structure of DrFam20C1 and hFam20A complex · the same entry in another collection · chain A against A, TM-score 1.00
Q96MK3 · AlphaFold monomer V2.0 prediction for pseudokinase FAM20A (Q96MK3) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q96MK3
Every structure of UniProt E7FBB8
Elsewhere: RCSB PDB 5YH2 · PDBe 5YH2 · UniProt Q96MK3 · UniProt E7FBB8

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