MolNFT v1 · #141637 · protein

Crystal structure of the nucleotide-free mutant A3B3

5ZEA · V-type sodium ATPase catalytic subunit a: “Crystal structure of the nucleotide-free mutant A3B3”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #141637 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5ZEA
Type: protein
Length: 6,235 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: V-type sodium ATPase catalytic subunit a; V-type sodium ATPase subunit B
EC: 3.6.3.15
UniProt: Q08636, Q08637
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 7 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	V-type sodium ATPase catalytic subunit a (EC 3.6.3.15)	protein	587	37% helix, 23% strand	Q08636
B, H	V-type sodium ATPase catalytic subunit a (EC 3.6.3.15)	protein	586	34% helix, 22% strand	Q08636
C, I	V-type sodium ATPase catalytic subunit a (EC 3.6.3.15)	protein	584	34% helix, 22% strand	Q08636
D, K	V-type sodium ATPase subunit B	protein	454	36% helix, 24% strand	Q08637
E	V-type sodium ATPase subunit B	protein	452	36% helix, 23% strand	Q08637
F	V-type sodium ATPase subunit B	protein	451	36% helix, 20% strand	Q08637
J, L	V-type sodium ATPase subunit B	protein	455	36% helix, 22% strand	Q08637

Ligands and binding sites

GOL · Glycerol · additive · 17 copies · chains A, E, C, D, G, H, K

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	1066	0.84	0.85	91	empty
2	1100	0.84	0.85	105	empty
3	929	0.84	0.86	88	empty
4	1047	0.84	0.85	87	empty
5	1033	0.84	0.85	90	empty

Interfaces

14 interfaces between chains.

I–L · 2244 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 2120 Å² buried · 26 hydrogen bonds · protein-protein
C–F · 2117 Å² buried · 21 hydrogen bonds · protein-protein
B–E · 2070 Å² buried · 25 hydrogen bonds · protein-protein
G–J · 2065 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5ZEA · Crystal structure of the nucleotide-free mutant A3B3 · the same entry in another collection · chain L against L, 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 Q08636
Every structure of UniProt Q08637
Elsewhere: RCSB PDB 5ZEA · PDBe 5ZEA · UniProt Q08636 · UniProt Q08637

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