MolNFT v1 · #84415 · protein

Crystal structure of the sodium binding rotor ring at pH 8.7

3ZK2 · ATP synthase subunit C: “Crystal structure of the sodium binding rotor ring at pH 8.7”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.79). MolNFT v1 #84415 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3ZK2
Type: protein
Length: 1,958 residues
Chains: 22
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit C
UniProt: Q8RGD7
Ligands: NA
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 91% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V	ATP synthase subunit C	protein	89	91% helix, 0% strand	Q8RGD7

Ligands and binding sites

NA · Sodium ion · metal · 22 copies · chains A, K, B, C, D, E, F, G, H, I, J, L, V, M, N, O, P, Q, R, S, T, U
DMU · Decyl-beta-D-maltopyranoside · additive · 23 copies · chains A, B, C, K, D, E, F, G, H, I, J, L, M, N, O, P, Q, R, S, T, U, V

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

Pockets

4 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	1001	0.79	0.79	68	empty
2	1068	0.78	0.79	76	empty
3	246	0.55	0.77	34	empty
4	117	0.42	0.76	21	empty

Interfaces

26 interfaces between chains.

E–F · 1967 Å² buried · 11 hydrogen bonds · protein-protein
A–K · 1960 Å² buried · 9 hydrogen bonds · protein-protein
F–G · 1955 Å² buried · 10 hydrogen bonds · protein-protein
P–Q · 1952 Å² buried · 11 hydrogen bonds · protein-protein
L–V · 1952 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3ZK2 · Crystal structure of the sodium binding rotor ring at pH 8.7 · the same entry in another collection · chain P against P, 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 Q8RGD7
Elsewhere: RCSB PDB 3ZK2 · PDBe 3ZK2 · UniProt Q8RGD7

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