MolNFT v1 · #30497 · protein

Crystal structure of kvap-33H1 fv complex

2A0L · Voltage-gated potassium channel: “Crystal structure of kvap-33H1 fv complex”. X-ray diffraction, 1 ligand (K), 13 pockets (best druggability 0.66). MolNFT v1 #30497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2A0L
Type: protein
Length: 870 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Voltage-gated potassium channel; 33H1 fv fragment
UniProt: Q9YDF8
Ligands: K
Pockets: 13 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Voltage-gated potassium channel	protein	214	64% helix, 0% strand	Q9YDF8
C, E	33H1 fv fragment	protein	105	0% helix, 35% strand	—
D, F	33H1 fv fragment	protein	116	3% helix, 50% strand	—

Ligands and binding sites

K · Potassium ion · metal · 4 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	439	0.66	0.77	29	empty
2	264	0.61	0.79	30	empty
3	215	0.59	0.80	33	empty
4	230	0.59	0.79	33	empty
5	59	0.44	0.82	21	empty

Interfaces

7 interfaces between chains.

A–B · 1466 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 787 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 777 Å² buried · 4 hydrogen bonds · protein-protein
B–F · 491 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 464 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2A0L · Crystal structure of KvAP-33H1 Fv complex · the same entry in another collection · chain C against C, TM-score 1.00
Q9YDF8 · AlphaFold monomer V2.0 prediction for voltage-gated potassium channel (Q9YDF8) · a predicted model of the same protein · chain A against A, TM-score 0.42

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 Q9YDF8
Elsewhere: RCSB PDB 2A0L · PDBe 2A0L · UniProt Q9YDF8

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