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Structure of human KV1.3 with Fab-shk fusion

Analyse Structure of human KV1.3 with Fab-shk fusion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SSV
Type: protein
Length: 1,874 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Potassium voltage-gated channel subfamily a member 3,GREEN fluorescent protein fusion…
UniProt: P22001
Ligands: K
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Potassium voltage-gated channel subfamily a member 3,GREEN fluorescent protein fusion	protein	350	61% helix, 5% strand	P22001
H	Fab-shk fusion, heavy chain	protein	261	10% helix, 37% strand	—
L	Fab-shk fusion, light chain	protein	213	7% helix, 43% strand	—

Ligands and binding sites

K · Potassium ion · metal · 3 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1125	0.83	0.84	84	empty
2	1080	0.80	0.82	123	empty
3	896	0.80	0.82	45	empty
4	610	0.78	0.84	80	empty
5	613	0.72	0.80	82	empty

Interfaces

11 interfaces between chains.

A–D · 2432 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2420 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 2345 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 2301 Å² buried · 12 hydrogen bonds · protein-protein
H–L · 976 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7SSV · Structure of human Kv1.3 with Fab-ShK fusion · the same entry in another collection · chain L against L, TM-score 1.00
P22001 · AlphaFold monomer V2.0 prediction for potassium voltage-gated channel subfamily a member… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P22001
Elsewhere: RCSB PDB 7SSV · PDBe 7SSV · UniProt P22001

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