MolNFT v1 · #167554 · protein

Chloroplast ATP synthase (O2, CF1FO)

6VOF · ATP synthase subunit alpha, chloroplastic: “Chloroplast ATP synthase (O2, CF1FO)”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.88). MolNFT v1 #167554 on GenesisL1: 3D structure, binding sites and…

PDB: 6VOF
Type: protein
Length: 5,175 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, P05435, P00833, P06453, P31853, P06451, P69447
Ligands: ATP, ADP
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 12 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	496	42% helix, 15% strand	P06450
B, C	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	501	41% helix, 14% strand	P06450
D	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	478	36% helix, 19% strand	P00825
E	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	479	37% helix, 18% strand	P00825
F	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	478	37% helix, 16% strand	P00825
d	ATP synthase delta chain, chloroplastic	protein	178	62% helix, 7% strand	P11402
g	ATP synthase gamma chain, chloroplastic	protein	321	52% helix, 10% strand	P05435
e	ATP synthase epsilon chain, chloroplastic	protein	130	24% helix, 32% strand	P00833
I	ATP synthase subunit B, chloroplastic	protein	151	95% helix, 0% strand	P06453
J	ATP synthase subunit B', chloroplastic	protein	136	93% helix, 0% strand	P31853
a	ATP synthase subunit a, chloroplastic	protein	220	67% helix, 1% strand	P06451
M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	ATP synthase subunit C, chloroplastic	protein	79	85% 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 · 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	1005	0.88	0.90	131	ATP
2	1079	0.88	0.89	251	empty
3	1140	0.88	0.89	149	ATP
4	1007	0.87	0.88	207	empty
5	429	0.84	0.92	59	ADP

Interfaces

51 interfaces between chains.

C–E · 2984 Å² buried · 43 hydrogen bonds · protein-protein
B–E · 2621 Å² buried · 28 hydrogen bonds · protein-protein
A–F · 2529 Å² buried · 45 hydrogen bonds · protein-protein
B–D · 2386 Å² buried · 45 hydrogen bonds · protein-protein
C–F · 2386 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 1 disulfide (covalent ligand, disulfide).

Compared structures

6VOF · Chloroplast ATP synthase (O2, CF1FO) · the same entry in another collection · chain I against I, 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 P05435
Every structure of UniProt P00833
Every structure of UniProt P06453
Every structure of UniProt P31853
Every structure of UniProt P06451
Every structure of UniProt P69447
Elsewhere: RCSB PDB 6VOF · PDBe 6VOF · UniProt P06450 · UniProt P00825 · UniProt P11402 · UniProt P05435 · UniProt P00833 · UniProt P06453 · UniProt P31853 · UniProt P06451 · UniProt P69447

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