Research workbench

Complete V1 complex from saccharomyces cerevisiae

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

PDB: 7TMM
Type: protein
Length: 5,236 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H(+)-transporting two-sector ATPase; Vacuolar proton pump subunit B; V-ATPase subunit E…
EC: 7.1.2.2
UniProt: A0A6L0YX77, A0A6A5Q585, A0A6A5Q7Y8, A0A6L0ZI53, A0A6A5Q1W2, A0A6A5PYF6, A0A6A5PTP1, P41807
Ligands: ADP
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 14 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H(+)-transporting two-sector ATPase (EC 7.1.2.2)	protein	593	37% helix, 24% strand	A0A6L0YX77
B	Vacuolar proton pump subunit B	protein	464	35% helix, 19% strand	A0A6A5Q585
C	H(+)-transporting two-sector ATPase (EC 7.1.2.2)	protein	592	37% helix, 23% strand	A0A6L0YX77
D, F	Vacuolar proton pump subunit B	protein	459	37% helix, 21% strand	A0A6A5Q585
E	H(+)-transporting two-sector ATPase (EC 7.1.2.2)	protein	576	35% helix, 23% strand	A0A6L0YX77
G, I	V-ATPase subunit E	protein	220	70% helix, 9% strand	A0A6A5Q7Y8
H	V-type proton ATPase subunit G	protein	109	89% helix, 0% strand	A0A6L0ZI53
J	V-type proton ATPase subunit G	protein	108	89% helix, 0% strand	A0A6L0ZI53
K	V-ATPase subunit E	protein	212	71% helix, 9% strand	A0A6A5Q7Y8
L	V-type proton ATPase subunit G	protein	99	86% helix, 0% strand	A0A6L0ZI53
M	V-type proton ATPase subunit D	protein	214	75% helix, 7% strand	A0A6A5Q1W2
N	V-type proton ATPase subunit F	protein	111	39% helix, 18% strand	A0A6A5PYF6
O	V-type proton ATPase subunit C	protein	359	53% helix, 8% strand	A0A6A5PTP1
P	V-type proton ATPase subunit H	protein	441	79% helix, 0% strand	P41807

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A, 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	909	0.89	0.91	163	empty
2	1049	0.88	0.89	107	empty
3	685	0.85	0.89	83	empty
4	910	0.84	0.86	105	empty
5	752	0.84	0.87	125	empty

Interfaces

34 interfaces between chains.

A–B · 3079 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 2491 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 2047 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 1895 Å² buried · 4 hydrogen bonds · protein-protein
D–K · 1874 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7TMM · Complete V1 Complex from Saccharomyces cerevisiae · 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 A0A6A5PTP1
Every structure of UniProt P41807
Elsewhere: RCSB PDB 7TMM · PDBe 7TMM · UniProt A0A6L0YX77 · UniProt A0A6A5Q585 · UniProt A0A6A5Q7Y8 · UniProt A0A6L0ZI53 · UniProt A0A6A5Q1W2 · UniProt A0A6A5PYF6 · UniProt A0A6A5PTP1 · UniProt P41807

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