MolNFT v1 · #127966 · protein

Shewanella denitrificans kef ctd in AMP bound form

5NC8 · Potassium efflux system protein: “Shewanella denitrificans kef ctd in AMP bound form”. X-ray diffraction, 1 ligand (AMP), 4 pockets (best druggability 0.51). MolNFT v1 #127966 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5NC8
Type: protein
Length: 317 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Potassium efflux system protein
UniProt: Q12SB3
Ligands: AMP
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Potassium efflux system protein	protein	159	50% helix, 18% strand	Q12SB3
B	Potassium efflux system protein	protein	158	51% helix, 16% strand	Q12SB3

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	263	0.51	0.75	41	empty
2	80	0.40	0.79	21	AMP
3	66	0.38	0.79	12	empty
4	63	0.34	0.77	20	AMP

Interfaces

1 interface between chains.

A–B · 2039 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5NC8 · Shewanella denitrificans Kef CTD in AMP bound form · 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 Q12SB3
Elsewhere: RCSB PDB 5NC8 · PDBe 5NC8 · UniProt Q12SB3

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