Research workbench

Chloroplast ATP synthase (R1, CF1FO)

Analyse Chloroplast ATP synthase (R1, CF1FO) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VON
Type: protein
Length: 5,186 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, TTX
Pockets: 20 · best druggability 0.88

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	501	39% helix, 18% strand	P06450
B	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	502	42% helix, 18% strand	P06450
C	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	500	41% helix, 18% strand	P06450
D	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	478	35% helix, 19% strand	P00825
E	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	481	36% helix, 20% strand	P00825
F	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	480	38% helix, 18% strand	P00825
d	ATP synthase delta chain, chloroplastic	protein	179	59% helix, 10% strand	P11402
g	ATP synthase gamma chain, chloroplastic	protein	322	56% helix, 7% strand	P05435
e	ATP synthase epsilon chain, chloroplastic	protein	131	28% helix, 30% strand	P00833
I	ATP synthase subunit B, chloroplastic	protein	153	96% helix, 0% strand	P06453
J	ATP synthase subunit B', chloroplastic	protein	130	93% helix, 0% strand	P31853
a	ATP synthase subunit a, chloroplastic	protein	223	67% helix, 0% strand	P06451
M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	ATP synthase subunit C, chloroplastic	protein	79	81% 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 E, A, F
TTX · Tentoxin · ligand · chains B, D

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	899	0.88	0.91	113	ATP
2	656	0.86	0.90	90	ATP
3	287	0.84	0.95	50	ADP
4	1099	0.84	0.85	100	ATP
5	900	0.83	0.84	104	empty

Interfaces

60 interfaces between chains.

A–F · 2938 Å² buried · 30 hydrogen bonds · protein-protein
C–F · 2359 Å² buried · 25 hydrogen bonds · protein-protein
I–J · 2297 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 2285 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 2210 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

6VON · Chloroplast ATP synthase (R1, 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 6VON · PDBe 6VON · UniProt P06450 · UniProt P00825 · UniProt P11402 · UniProt P05435 · UniProt P00833 · UniProt P06453 · UniProt P31853 · UniProt P06451 · UniProt P69447

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