Research workbench

Mycobacterium smegmatis ATP synthase rotor state 2

Analyse Mycobacterium smegmatis ATP synthase rotor state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NKK
Type: protein
Length: 1,143 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP synthase subunit alpha; ATP synthase gamma chain; ATP synthase epsilon chain; ATP…
EC: 7.1.2.2
UniProt: A0R202, A0R201, A0R1Z9, A0R205
Pockets: 9 · best druggability 0.84

Structure

electron microscopy · 6 distinct chains · 59% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	ATP synthase subunit alpha (EC 7.1.2.2)	protein	14	0% helix, 57% strand	A0R202
G	ATP synthase gamma chain	protein	246	52% helix, 19% strand	A0R201
H	ATP synthase epsilon chain	protein	118	18% helix, 45% strand	A0R1Z9
L, M, O, Q, R, S, T	ATP synthase subunit C	protein	85	88% helix, 0% strand	A0R205
N	ATP synthase subunit C	protein	84	88% helix, 0% strand	A0R205
P	ATP synthase subunit C	protein	86	84% helix, 0% strand	A0R205

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	812	0.84	0.85	64	empty
2	231	0.70	0.85	27	empty
3	184	0.61	0.83	31	empty
4	250	0.51	0.75	39	empty
5	62	0.43	0.82	18	empty

Interfaces

24 interfaces between chains.

L–T · 1766 Å² buried · 13 hydrogen bonds · protein-protein
R–S · 1735 Å² buried · 13 hydrogen bonds · protein-protein
P–Q · 1723 Å² buried · 4 hydrogen bonds · protein-protein
M–N · 1711 Å² buried · 11 hydrogen bonds · protein-protein
Q–R · 1701 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7NKK · Mycobacterium smegmatis ATP synthase rotor state 2 · the same entry in another collection · chain T against T, 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 A0R201
Every structure of UniProt A0R1Z9
Every structure of UniProt A0R205
Elsewhere: RCSB PDB 7NKK · PDBe 7NKK · UniProt A0R202 · UniProt A0R201 · UniProt A0R1Z9 · UniProt A0R205

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