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Complete ion-coordination structure in the rotor ring of na- dependent F-ATP synthase

Analyse Complete ion-coordination structure in the rotor ring of na- dependent F-ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WGM
Type: protein
Length: 3,916 residues
Chains: 44
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit C, sodium ion specific
UniProt: Q8KRV3
Ligands: F09, NA
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 87% 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, 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, sodium ion specific	protein	89	87% helix, 0% strand	Q8KRV3

Ligands and binding sites

F09 · Nonan-1-ol · ligand · 44 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v
NA · Sodium ion · metal · 44 copies · chains A, K, B, C, D, E, F, G, H, I, J, L, V, M, N, O, P, Q, R, S, T, U, a, k, b, c, d, e, f, g, h, i, j, l, v, m, n, o, p, q, r, s, t, u

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

Pockets

6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	765	0.75	0.78	63	empty
2	732	0.75	0.78	53	empty
3	642	0.73	0.78	40	empty
4	584	0.72	0.78	43	empty
5	647	0.65	0.74	66	empty

Interfaces

110 interfaces between chains.

O–P · 1971 Å² buried · 11 hydrogen bonds · protein-protein
l–m · 1965 Å² buried · 11 hydrogen bonds · protein-protein
e–f · 1965 Å² buried · 15 hydrogen bonds · protein-protein
o–p · 1965 Å² buried · 10 hydrogen bonds · protein-protein
J–K · 1963 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2WGM · Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase · the same entry in another collection · chain K against K, 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 Q8KRV3
Elsewhere: RCSB PDB 2WGM · PDBe 2WGM · UniProt Q8KRV3

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