MolNFT v1 · #28376 · protein

Structure of the rotor ring of F-type na+-ATPase from ilyobacter tartaricus

1YCE · Subunit C: “Structure of the rotor ring of F-type na+-ATPase from ilyobacter tartaricus”. X-ray diffraction, 2 ligands (F09, NA), 7 pockets (best druggability 0.73). MolNFT v1 #28376 on GenesisL1: 3D structure, binding sites and…

PDB: 1YCE
Type: protein
Length: 3,916 residues
Chains: 44
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Subunit C
Ligands: F09, NA
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 90% 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	Subunit C	protein	89	90% helix, 0% strand	—

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

7 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	655	0.73	0.78	57	empty
2	591	0.72	0.78	53	empty
3	541	0.71	0.78	39	empty
4	510	0.70	0.78	42	empty
5	706	0.65	0.74	66	empty

Interfaces

110 interfaces between chains.

a–b · 1979 Å² buried · 12 hydrogen bonds · protein-protein
q–r · 1968 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1964 Å² buried · 14 hydrogen bonds · protein-protein
f–g · 1959 Å² buried · 14 hydrogen bonds · protein-protein
H–I · 1955 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1YCE · Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 1YCE · PDBe 1YCE

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