Research workbench

V1 complex lacking subunit C from saccharomyces cerevisiae, state 2

Analyse V1 complex lacking subunit C from saccharomyces cerevisiae, state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TMP
Type: protein
Length: 4,805 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-ATPase subunit E…
EC: 7.1.2.2
UniProt: A0A6L0YX77, A0A6A5Q585, A0A6A5Q7Y8, A0A6L0ZI53, A0A6A5Q1W2, A0A6A5PYF6, P41807
Ligands: ADP, MG
Pockets: 20 · best druggability 0.90

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	593	39% helix, 22% strand	A0A6L0YX77
B	Vacuolar proton pump subunit B	protein	464	35% helix, 20% strand	A0A6A5Q585
C	H(+)-transporting two-sector ATPase (EC 7.1.2.2)	protein	592	36% helix, 23% strand	A0A6L0YX77
D, F	Vacuolar proton pump subunit B	protein	459	37% helix, 22% strand	A0A6A5Q585
E	H(+)-transporting two-sector ATPase (EC 7.1.2.2)	protein	590	35% helix, 23% strand	A0A6L0YX77
G	V-ATPase subunit E	protein	187	66% helix, 10% strand	A0A6A5Q7Y8
H	V-type proton ATPase subunit G	protein	86	86% helix, 0% strand	A0A6L0ZI53
I	V-ATPase subunit E	protein	217	69% helix, 10% strand	A0A6A5Q7Y8
J	V-type proton ATPase subunit G	protein	108	89% helix, 0% strand	A0A6L0ZI53
K	V-ATPase subunit E	protein	196	66% 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, 13% strand	A0A6A5PYF6
P	V-type proton ATPase subunit H	protein	441	78% helix, 0% strand	P41807

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A, B
MG · Magnesium ion · metal · chains A

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	1142	0.90	0.93	182	empty
2	1068	0.86	0.87	164	empty
3	577	0.84	0.89	48	empty
4	1197	0.83	0.84	156	empty
5	697	0.83	0.87	64	empty

Interfaces

28 interfaces between chains.

A–B · 3094 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 2622 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2166 Å² buried · 33 hydrogen bonds · protein-protein
B–I · 2053 Å² buried · 14 hydrogen bonds · protein-protein
D–K · 2017 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7TMP · V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2 · 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 7TMP · PDBe 7TMP · UniProt A0A6L0YX77 · UniProt A0A6A5Q585 · UniProt A0A6A5Q7Y8 · UniProt A0A6L0ZI53 · UniProt A0A6A5Q1W2 · UniProt A0A6A5PYF6 · UniProt P41807

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