Research workbench

Thermus thermophilus V/A-type ATPASE/SYNTHASE, rotational state 3

Analyse Thermus thermophilus V/A-type ATPASE/SYNTHASE, rotational state 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R0Y
Type: protein
Length: 5,845 residues
Chains: 26
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: V-type ATP synthase alpha chain; V-type ATP synthase beta chain; V-type ATP synthase…
EC: 7.1.2.2
UniProt: Q56403, Q56404, O87880, P74903, Q5SIT5, P74901, P74902, Q5SIT6, Q5SIT7
Ligands: ADP, MG
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 15 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	V-type ATP synthase alpha chain (EC 7.1.2.2)	protein	577	30% helix, 20% strand	Q56403
D	V-type ATP synthase beta chain	protein	461	32% helix, 20% strand	Q56404
E	V-type ATP synthase beta chain	protein	462	32% helix, 21% strand	Q56404
F	V-type ATP synthase beta chain	protein	461	30% helix, 20% strand	Q56404
G	V-type ATP synthase subunit D	protein	206	73% helix, 7% strand	O87880
H	V-type ATP synthase subunit F	protein	104	38% helix, 13% strand	P74903
I	V-type ATP synthase, subunit (vapc-therm)	protein	103	94% helix, 0% strand	Q5SIT5
J	V-type ATP synthase subunit E	protein	186	75% helix, 11% strand	P74901
K	V-type ATP synthase, subunit (vapc-therm)	protein	99	91% helix, 0% strand	Q5SIT5
L	V-type ATP synthase subunit E	protein	187	68% helix, 7% strand	P74901
M	V-type ATP synthase subunit C	protein	320	63% helix, 0% strand	P74902
N	V-type ATP synthase subunit I	protein	649	59% helix, 7% strand	Q5SIT6
O, P, R, S, T, U, V, W, Y, Z	V-type ATP synthase, subunit K	protein	73	89% helix, 0% strand	Q5SIT7
Q	V-type ATP synthase, subunit K	protein	74	84% helix, 0% strand	Q5SIT7
X	V-type ATP synthase, subunit K	protein	72	93% helix, 0% strand	Q5SIT7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, D
MG · Magnesium ion · metal · chains B

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	1010	0.90	0.92	141	empty
2	559	0.85	0.90	56	empty
3	1113	0.84	0.84	105	empty
4	831	0.83	0.85	97	empty
5	1066	0.82	0.84	108	empty

Interfaces

49 interfaces between chains.

B–D · 3340 Å² buried · 37 hydrogen bonds · protein-protein
A–F · 2921 Å² buried · 24 hydrogen bonds · protein-protein
C–E · 2495 Å² buried · 38 hydrogen bonds · protein-protein
K–L · 2414 Å² buried · 21 hydrogen bonds · protein-protein
I–J · 2413 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6R0Y · Thermus thermophilus V/A-type ATPase/synthase, rotational state 3 · the same entry in another collection · chain K against K, 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 Q56403
Every structure of UniProt Q56404
Every structure of UniProt O87880
Every structure of UniProt P74903
Every structure of UniProt Q5SIT5
Every structure of UniProt P74901
Every structure of UniProt P74902
Every structure of UniProt Q5SIT6
Every structure of UniProt Q5SIT7
Elsewhere: RCSB PDB 6R0Y · PDBe 6R0Y · UniProt Q56403 · UniProt Q56404 · UniProt O87880 · UniProt P74903 · UniProt Q5SIT5 · UniProt P74901 · UniProt P74902 · UniProt Q5SIT6 · UniProt Q5SIT7

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