MolNFT v1 · #167558 · protein

Chloroplast ATP synthase (R3, CF1FO)

6VOJ · ATP synthase subunit alpha, chloroplastic: “Chloroplast ATP synthase (R3, CF1FO)”. Electron microscopy, 3 ligands (ATP, ADP, TTX), 20 pockets (best druggability 0.87). MolNFT v1 #167558 on GenesisL1: 3D structure, binding sites and…

PDB: 6VOJ
Type: protein
Length: 5,185 residues
Chains: 26
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha, chloroplastic; ATP synthase subunit beta, chloroplastic; ATP…
EC: 7.1.2.2
UniProt: P06450, P00825, P11402, P00833, P05435, P06453, P31853, P06451, P69447
Ligands: ATP, ADP, TTX
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 13 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	498	42% helix, 17% strand	P06450
B	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	501	39% helix, 14% strand	P06450
C	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	501	40% helix, 17% strand	P06450
D	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	480	36% helix, 19% strand	P00825
E	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	478	36% helix, 19% strand	P00825
F	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	479	35% helix, 18% strand	P00825
d	ATP synthase delta chain, chloroplastic	protein	179	59% helix, 13% strand	P11402
e	ATP synthase epsilon chain, chloroplastic	protein	131	30% helix, 33% strand	P00833
g	ATP synthase gamma chain, chloroplastic	protein	322	54% helix, 7% strand	P05435
I	ATP synthase subunit B, chloroplastic	protein	154	92% helix, 0% strand	P06453
J	ATP synthase subunit B', chloroplastic	protein	134	96% helix, 0% strand	P31853
a	ATP synthase subunit a, chloroplastic	protein	222	68% helix, 3% strand	P06451
M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	ATP synthase subunit C, chloroplastic	protein	79	87% helix, 0% strand	P69447

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, E, C, F
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, D, F
TTX · Tentoxin · ligand · chains C, E

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	1086	0.87	0.88	112	ATP
2	784	0.86	0.89	102	empty
3	694	0.84	0.88	76	ATP
4	1165	0.83	0.84	108	ATP
5	482	0.83	0.90	76	ADP

Interfaces

63 interfaces between chains.

B–D · 2870 Å² buried · 34 hydrogen bonds · protein-protein
I–J · 2487 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 2354 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 2349 Å² buried · 26 hydrogen bonds · protein-protein
C–E · 2253 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6VOJ · Chloroplast ATP synthase (R3, CF1FO) · the same entry in another collection · chain g against g, 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 P06450
Every structure of UniProt P00825
Every structure of UniProt P11402
Every structure of UniProt P00833
Every structure of UniProt P05435
Every structure of UniProt P06453
Every structure of UniProt P31853
Every structure of UniProt P06451
Every structure of UniProt P69447
Elsewhere: RCSB PDB 6VOJ · PDBe 6VOJ · UniProt P06450 · UniProt P00825 · UniProt P11402 · UniProt P00833 · UniProt P05435 · UniProt P06453 · UniProt P31853 · UniProt P06451 · UniProt P69447

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