MolNFT v1 · #114655 · protein

Crystal structure of yeast V1-ATPase in the autoinhibited form

5BW9 · V-type proton ATPase catalytic subunit a: “Crystal structure of yeast V1-ATPase in the autoinhibited form”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #114655 on GenesisL1: 3D structure, binding sites and…

PDB: 5BW9
Type: protein
Length: 9,074 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: V-type proton ATPase catalytic subunit a; V-type proton ATPase subunit B; V-type proton…
EC: 3.6.3.14, 3.1.-.-
UniProt: P17255, P16140, P41807, P32610, P48836, P22203
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 27 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, a	V-type proton ATPase catalytic subunit a (EC 3.6.3.14, 3.1.-.-)	protein	591	32% helix, 22% strand	P17255
B	V-type proton ATPase catalytic subunit a (EC 3.6.3.14, 3.1.-.-)	protein	594	33% helix, 24% strand	P17255
C	V-type proton ATPase catalytic subunit a (EC 3.6.3.14, 3.1.-.-)	protein	589	33% helix, 22% strand	P17255
D	V-type proton ATPase subunit B	protein	457	32% helix, 21% strand	P16140
E	V-type proton ATPase subunit B	protein	453	35% helix, 22% strand	P16140
F	V-type proton ATPase subunit B	protein	449	33% helix, 20% strand	P16140
H	V-type proton ATPase subunit H	protein	445	68% helix, 0% strand	P41807
G	V-type proton ATPase subunit D	protein	139	88% helix, 0% strand	P32610
J	V-type proton ATPase subunit G	protein	104	92% helix, 0% strand	P48836
I	V-type proton ATPase subunit E	protein	216	74% helix, 6% strand	P22203
K	V-type proton ATPase subunit E	protein	178	66% helix, 12% strand	P22203
L	V-type proton ATPase subunit G	protein	68	93% helix, 0% strand	P48836
M	V-type proton ATPase subunit E	protein	203	71% helix, 7% strand	P22203
N	V-type proton ATPase subunit G	protein	81	83% helix, 0% strand	P48836
h	V-type proton ATPase subunit H	protein	444	68% helix, 0% strand	P41807
g	V-type proton ATPase subunit D	protein	141	87% helix, 0% strand	P32610
i	V-type proton ATPase subunit E	protein	217	74% helix, 7% strand	P22203
j	V-type proton ATPase subunit G	protein	101	95% helix, 0% strand	P48836
l	V-type proton ATPase subunit G	protein	66	92% helix, 0% strand	P48836
k	V-type proton ATPase subunit E	protein	168	64% helix, 13% strand	P22203
b	V-type proton ATPase catalytic subunit a (EC 3.6.3.14, 3.1.-.-)	protein	589	33% helix, 24% strand	P17255
c	V-type proton ATPase catalytic subunit a (EC 3.6.3.14, 3.1.-.-)	protein	586	33% helix, 22% strand	P17255
d	V-type proton ATPase subunit B	protein	460	32% helix, 20% strand	P16140
e	V-type proton ATPase subunit B	protein	456	35% helix, 22% strand	P16140
f	V-type proton ATPase subunit B	protein	449	33% helix, 20% strand	P16140
m	V-type proton ATPase subunit E	protein	181	67% helix, 9% strand	P22203
n	V-type proton ATPase subunit G	protein	58	88% helix, 0% strand	P48836

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	1076	0.85	0.87	200	empty
2	1017	0.85	0.86	168	empty
3	946	0.84	0.86	158	empty
4	750	0.83	0.87	133	empty
5	777	0.83	0.87	114	empty

Interfaces

43 interfaces between chains.

B–E · 1297 Å² buried · 7 hydrogen bonds · protein-protein
b–e · 1266 Å² buried · 7 hydrogen bonds · protein-protein
c–f · 1050 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1043 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 1029 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5BW9 · Crystal Structure of Yeast V1-ATPase in the Autoinhibited Form · the same entry in another collection · chain I against I, 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 P17255
Every structure of UniProt P16140
Every structure of UniProt P41807
Every structure of UniProt P32610
Every structure of UniProt P48836
Every structure of UniProt P22203
Elsewhere: RCSB PDB 5BW9 · PDBe 5BW9 · UniProt P17255 · UniProt P16140 · UniProt P41807 · UniProt P32610 · UniProt P48836 · UniProt P22203

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