MolNFT v1 · #177125 · protein

Cryoem structure of human KV4.2-DPP6S complex

7E8B · Dipeptidyl aminopeptidase-like protein 6: “Cryoem structure of human KV4.2-DPP6S complex”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #177125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7E8B
Type: protein
Length: 4,580 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptidyl aminopeptidase-like protein 6; Potassium voltage-gated channel subfamily D…
UniProt: P42658, Q9NZV8
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 3 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, K, J, I	Dipeptidyl aminopeptidase-like protein 6	protein	757	16% helix, 28% strand	P42658
B, D	Potassium voltage-gated channel subfamily D member 2	protein	388	62% helix, 4% strand	Q9NZV8
A, C	Potassium voltage-gated channel subfamily D member 2	protein	388	65% helix, 2% strand	Q9NZV8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	895	0.85	0.87	103	empty
2	785	0.84	0.87	68	empty
3	570	0.74	0.81	67	empty
4	777	0.72	0.77	74	empty
5	742	0.71	0.77	75	empty

Interfaces

12 interfaces between chains.

B–A · 2787 Å² buried · 27 hydrogen bonds · protein-protein
D–C · 2785 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 2731 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 2723 Å² buried · 25 hydrogen bonds · protein-protein
L–K · 1882 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

7E8B · CryoEM structure of human Kv4.2-DPP6S complex · the same entry in another collection · chain C against C, TM-score 1.00
P42658 · AlphaFold monomer V2.0 prediction for dipeptidyl aminopeptidase-like protein 6 (P42658) · a predicted model of the same protein · chain I against A, TM-score 0.97

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 P42658
Every structure of UniProt Q9NZV8
Elsewhere: RCSB PDB 7E8B · PDBe 7E8B · UniProt P42658 · UniProt Q9NZV8

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