MolNFT v1 · #161113 · protein

F1-ATPase from fusobacterium nucleatum

6Q45 · ATP synthase subunit alpha: “F1-ATPase from fusobacterium nucleatum”. X-ray diffraction, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #161113 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Q45
Type: protein
Length: 6,420 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain; ATP…
UniProt: Q8RGE0, Q8RGE2, Q8RGE1, Q8RGE3
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 10 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha	protein	476	41% helix, 22% strand	Q8RGE0
B, I	ATP synthase subunit alpha	protein	474	41% helix, 20% strand	Q8RGE0
C	ATP synthase subunit alpha	protein	471	41% helix, 21% strand	Q8RGE0
D, E, N	ATP synthase subunit beta	protein	460	39% helix, 21% strand	Q8RGE2
F	ATP synthase subunit beta	protein	462	39% helix, 21% strand	Q8RGE2
G, O	ATP synthase gamma chain	protein	281	59% helix, 11% strand	Q8RGE1
H, P	ATP synthase epsilon chain	protein	134	31% helix, 37% strand	Q8RGE3
J	ATP synthase subunit alpha	protein	469	41% helix, 20% strand	Q8RGE0
K	ATP synthase subunit alpha	protein	466	41% helix, 21% strand	Q8RGE0
L, M	ATP synthase subunit beta	protein	459	39% helix, 21% strand	Q8RGE2

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, D, B, C, F, I, L, J, K, N
ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains C, D, B, F, K, L, J, N
MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, F, I, J, K, L, N

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1009	0.88	0.89	122	ATP, MG
2	663	0.87	0.92	94	ATP, MG
3	919	0.86	0.88	107	empty
4	921	0.86	0.88	100	ATP, MG
5	825	0.86	0.88	93	ATP, MG

Interfaces

31 interfaces between chains.

K–L · 2722 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2536 Å² buried · 29 hydrogen bonds · protein-protein
I–L · 2419 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 2376 Å² buried · 26 hydrogen bonds · protein-protein
C–F · 2371 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

6Q45 · F1-ATPase from Fusobacterium nucleatum · 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 Q8RGE0
Every structure of UniProt Q8RGE2
Every structure of UniProt Q8RGE1
Every structure of UniProt Q8RGE3
Elsewhere: RCSB PDB 6Q45 · PDBe 6Q45 · UniProt Q8RGE0 · UniProt Q8RGE2 · UniProt Q8RGE1 · UniProt Q8RGE3

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