Research workbench

Chloroplast ATP synthase (C1, CF1FO)

Analyse Chloroplast ATP synthase (C1, CF1FO) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VMB
Type: protein
Length: 5,194 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, P06453, P31853, P06451, P11402, P00833, P05435, P69447
Ligands: ATP, ADP
Pockets: 20 · best druggability 0.90

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	501	43% helix, 17% strand	P06450
B	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	503	39% helix, 14% strand	P06450
C	ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2)	protein	500	42% helix, 16% strand	P06450
D	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	478	34% helix, 15% strand	P00825
E	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	481	35% helix, 15% strand	P00825
F	ATP synthase subunit beta, chloroplastic (EC 7.1.2.2)	protein	480	36% helix, 17% strand	P00825
I	ATP synthase subunit B, chloroplastic	protein	153	96% helix, 0% strand	P06453
J	ATP synthase subunit B', chloroplastic	protein	136	95% helix, 0% strand	P31853
a	ATP synthase subunit a, chloroplastic	protein	223	68% helix, 0% strand	P06451
d	ATP synthase delta chain, chloroplastic	protein	179	61% helix, 12% strand	P11402
e	ATP synthase epsilon chain, chloroplastic	protein	131	24% helix, 30% strand	P00833
g	ATP synthase gamma chain, chloroplastic	protein	323	53% helix, 11% strand	P05435
Z, Y, X, W, V, U, T, S, P, O, N, M, Q, R	ATP synthase subunit C, chloroplastic	protein	79	86% helix, 0% strand	P69447

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, D, A, F

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	981	0.90	0.92	133	ATP
2	749	0.84	0.87	176	empty
3	637	0.84	0.88	73	ATP
4	784	0.83	0.86	89	ATP
5	471	0.82	0.89	74	ADP

Interfaces

51 interfaces between chains.

A–F · 2855 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 2413 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 2264 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 2206 Å² buried · 25 hydrogen bonds · protein-protein
C–E · 1999 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6VMB · Chloroplast ATP synthase (C1, CF1FO) · the same entry in another collection · chain J against J, 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 P06453
Every structure of UniProt P31853
Every structure of UniProt P06451
Every structure of UniProt P11402
Every structure of UniProt P00833
Every structure of UniProt P05435
Every structure of UniProt P69447
Elsewhere: RCSB PDB 6VMB · PDBe 6VMB · UniProt P06450 · UniProt P00825 · UniProt P06453 · UniProt P31853 · UniProt P06451 · UniProt P11402 · UniProt P00833 · UniProt P05435 · UniProt P69447

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