Research workbench

Mycobacterium smegmatis ATP synthase state 1E

Analyse Mycobacterium smegmatis ATP synthase state 1E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NJO
Type: protein
Length: 4,934 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain; ATP…
EC: 7.1.2.2
UniProt: A0R202, A0R200, A0R201, A0R1Z9, A0R205, A0R206, A0R204, A0R203
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 14 distinct chains · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP synthase subunit alpha (EC 7.1.2.2)	protein	507	40% helix, 19% strand	A0R202
B	ATP synthase subunit alpha (EC 7.1.2.2)	protein	505	43% helix, 20% strand	A0R202
C	ATP synthase subunit alpha (EC 7.1.2.2)	protein	533	41% helix, 19% strand	A0R202
D	ATP synthase subunit beta (EC 7.1.2.2)	protein	468	40% helix, 22% strand	A0R200
E	ATP synthase subunit beta (EC 7.1.2.2)	protein	464	40% helix, 23% strand	A0R200
F	ATP synthase subunit beta (EC 7.1.2.2)	protein	469	40% helix, 22% strand	A0R200
G	ATP synthase gamma chain	protein	296	62% helix, 14% strand	A0R201
H	ATP synthase epsilon chain	protein	118	19% helix, 49% strand	A0R1Z9
L, M, N, T	ATP synthase subunit C	protein	84	89% helix, 0% strand	A0R205
O, S	ATP synthase subunit C	protein	83	87% helix, 0% strand	A0R205
P, Q, R	ATP synthase subunit C	protein	85	80% helix, 0% strand	A0R205
a	ATP synthase subunit a	protein	238	71% helix, 5% strand	A0R206
b	ATP synthase subunit B	protein	141	91% helix, 0% strand	A0R204
d	ATP synthase subunit B-delta	protein	438	77% helix, 5% strand	A0R203

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 C, D, E
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, 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	582	0.87	0.92	83	empty
2	500	0.85	0.92	85	empty
3	1173	0.85	0.86	108	ATP, MG
4	947	0.84	0.86	76	ATP, MG
5	837	0.84	0.86	66	empty

Interfaces

50 interfaces between chains.

C–D · 2869 Å² buried · 35 hydrogen bonds · protein-protein
A–E · 2301 Å² buried · 26 hydrogen bonds · protein-protein
B–F · 2278 Å² buried · 31 hydrogen bonds · protein-protein
b–d · 2277 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 2248 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

7NJO · Mycobacterium smegmatis ATP synthase state 1e · the same entry in another collection · chain N against N, 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 A0R202
Every structure of UniProt A0R200
Every structure of UniProt A0R201
Every structure of UniProt A0R1Z9
Every structure of UniProt A0R205
Every structure of UniProt A0R206
Every structure of UniProt A0R204
Every structure of UniProt A0R203
Elsewhere: RCSB PDB 7NJO · PDBe 7NJO · UniProt A0R202 · UniProt A0R200 · UniProt A0R201 · UniProt A0R1Z9 · UniProt A0R205 · UniProt A0R206 · UniProt A0R204 · UniProt A0R203

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