Research workbench

V1 complex lacking subunit C from saccharomyces cerevisiae, state 1

Analyse V1 complex lacking subunit C from saccharomyces cerevisiae, state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TMO
Type: protein
Length: 4,816 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H(+)-transporting two-sector ATPase; Vacuolar proton pump subunit B; V-type proton ATPase…
EC: 7.1.2.2
UniProt: A0A6L0YX77, A0A6A5Q585, A0A6A5Q7Y8, A0A6L0ZI53, A0A6A5Q1W2, A0A6A5PYF6, P41807
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 14 distinct chains · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H(+)-transporting two-sector ATPase (EC 7.1.2.2)	protein	592	37% helix, 22% strand	A0A6L0YX77
B	Vacuolar proton pump subunit B	protein	464	33% helix, 23% strand	A0A6A5Q585
C	H(+)-transporting two-sector ATPase (EC 7.1.2.2)	protein	585	38% helix, 23% strand	A0A6L0YX77
D, F	Vacuolar proton pump subunit B	protein	459	36% helix, 22% strand	A0A6A5Q585
E	H(+)-transporting two-sector ATPase (EC 7.1.2.2)	protein	590	36% helix, 21% strand	A0A6L0YX77
G	V-type proton ATPase subunit E	protein	200	69% helix, 10% strand	A0A6A5Q7Y8
H	V-type proton ATPase subunit G	protein	82	82% helix, 0% strand	A0A6L0ZI53
I	V-type proton ATPase subunit E	protein	217	68% helix, 6% strand	A0A6A5Q7Y8
J	V-type proton ATPase subunit G	protein	108	89% helix, 0% strand	A0A6L0ZI53
K	V-type proton ATPase subunit E	protein	206	70% helix, 9% strand	A0A6A5Q7Y8
L	V-type proton ATPase subunit G	protein	88	86% helix, 0% strand	A0A6L0ZI53
M	V-type proton ATPase subunit D	protein	214	74% helix, 7% strand	A0A6A5Q1W2
N	V-type proton ATPase subunit F	protein	111	36% helix, 18% strand	A0A6A5PYF6
P	V-type proton ATPase subunit H	protein	441	79% helix, 0% strand	P41807

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A, B
ADP · Adenosine-5'-diphosphate · ligand · chains E, F
MG · Magnesium ion · metal · 2 copies · chains A, E

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	1141	0.89	0.91	156	empty
2	1076	0.87	0.88	95	empty
3	1010	0.86	0.87	165	empty
4	790	0.84	0.87	116	ADP, MG
5	560	0.84	0.90	57	empty

Interfaces

29 interfaces between chains.

A–B · 3194 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 2638 Å² buried · 28 hydrogen bonds · protein-protein
B–G · 2080 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1934 Å² buried · 14 hydrogen bonds · protein-protein
F–K · 1873 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7TMO · V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1 · the same entry in another collection · chain P against P, 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 A0A6L0YX77
Every structure of UniProt A0A6A5Q585
Every structure of UniProt A0A6A5Q7Y8
Every structure of UniProt A0A6L0ZI53
Every structure of UniProt A0A6A5Q1W2
Every structure of UniProt A0A6A5PYF6
Every structure of UniProt P41807
Elsewhere: RCSB PDB 7TMO · PDBe 7TMO · UniProt A0A6L0YX77 · UniProt A0A6A5Q585 · UniProt A0A6A5Q7Y8 · UniProt A0A6L0ZI53 · UniProt A0A6A5Q1W2 · UniProt A0A6A5PYF6 · UniProt P41807

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