MolNFT v1 · #123100 · protein

Kcsa in vitro

5J9P · Fab: “Kcsa in vitro”. X-ray diffraction, 1 ligand (K), 5 pockets (best druggability 0.69). MolNFT v1 #123100 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5J9P
Type: protein
Length: 527 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab; PH-gated potassium channel kcsa
UniProt: P0A334
Ligands: K
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab	protein	219	4% helix, 48% strand	—
B	Fab	protein	212	7% helix, 49% strand	—
C	PH-gated potassium channel kcsa	protein	96	70% helix, 0% strand	P0A334

Ligands and binding sites

K · Potassium ion · metal · 6 copies · chains C

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	695	0.69	0.77	57	empty
2	60	0.53	0.87	18	empty
3	73	0.52	0.85	16	empty
4	146	0.48	0.78	26	empty
5	90	0.34	0.74	21	empty

Interfaces

3 interfaces between chains.

A–B · 1832 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 464 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 437 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5J9P · KcsA in vitro · the same entry in another collection · chain A against A, TM-score 1.00

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 P0A334
Elsewhere: RCSB PDB 5J9P · PDBe 5J9P · UniProt P0A334

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