Research workbench

Chloroplast F1FO conformation 3

Analyse Chloroplast F1FO conformation 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FKI
Type: protein
Length: 5,201 residues
Chains: 26
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit a, chloroplastic; ATP synthase subunit B, chloroplastic; ATP…
EC: 3.6.3.14
UniProt: P06451, P06453, P11402, P31853, P00833, P05435, P69447, P06450, P00825
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 13 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	ATP synthase subunit a, chloroplastic	protein	223	68% helix, 4% strand	P06451
b	ATP synthase subunit B, chloroplastic	protein	161	90% helix, 1% strand	P06453
d	ATP synthase delta chain, chloroplastic	protein	179	63% helix, 15% strand	P11402
p	ATP synthase subunit B', chloroplastic	protein	143	90% helix, 0% strand	P31853
e	ATP synthase epsilon chain, chloroplastic	protein	131	29% helix, 36% strand	P00833
g	ATP synthase gamma chain, chloroplastic	protein	321	54% helix, 15% strand	P05435
S, N, O, P, Q, R, M, T, G, H, L, K, J, I	ATP synthase subunit C, chloroplastic	protein	79	89% helix, 0% strand	P69447
E	ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14)	protein	498	44% helix, 18% strand	P06450
F	ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)	protein	479	38% helix, 20% strand	P00825
A	ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14)	protein	501	40% helix, 19% strand	P06450
B	ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)	protein	478	40% helix, 20% strand	P00825
C	ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14)	protein	501	40% helix, 19% strand	P06450
D	ATP synthase subunit beta, chloroplastic (EC 3.6.3.14)	protein	480	39% helix, 20% strand	P00825

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains E, D, F, A, B, C
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 5 copies · chains E, A, B, C, 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	1156	0.88	0.89	128	ATP, MG
2	674	0.86	0.90	101	empty
3	873	0.83	0.85	86	ATP, MG
4	989	0.81	0.83	81	ATP, MG
5	477	0.81	0.88	64	ADP, MG

Interfaces

63 interfaces between chains.

b–p · 2981 Å² buried · 115 hydrogen bonds · protein-protein
C–D · 2928 Å² buried · 40 hydrogen bonds · protein-protein
E–D · 2372 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 2353 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 2120 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

6FKI · Chloroplast F1Fo conformation 3 · the same entry in another collection · chain Q against Q, 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 P06451
Every structure of UniProt P06453
Every structure of UniProt P11402
Every structure of UniProt P31853
Every structure of UniProt P00833
Every structure of UniProt P05435
Every structure of UniProt P69447
Every structure of UniProt P06450
Every structure of UniProt P00825
Elsewhere: RCSB PDB 6FKI · PDBe 6FKI · UniProt P06451 · UniProt P06453 · UniProt P11402 · UniProt P31853 · UniProt P00833 · UniProt P05435 · UniProt P69447 · UniProt P06450 · UniProt P00825

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