MolNFT v1 · #124878 · protein

Crystal structure of a plasma membrane proton pump

5KSD · ATPase 2, plasma membrane-type: “Crystal structure of a plasma membrane proton pump”. X-ray diffraction, 3 ligands (ACP, MG, K), 20 pockets (best druggability 0.78). MolNFT v1 #124878 on GenesisL1: 3D structure, binding sites and…

PDB: 5KSD
Type: protein
Length: 1,666 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATPase 2, plasma membrane-type
EC: 3.6.3.6
UniProt: P19456
Ligands: ACP, MG, K
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ATPase 2, plasma membrane-type (EC 3.6.3.6)	protein	833	51% helix, 14% strand	P19456

Ligands and binding sites

ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B
LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	653	0.78	0.84	65	MG, ACP
2	363	0.75	0.86	44	MG, ACP
3	77	0.75	0.98	28	empty
4	290	0.73	0.86	50	empty
5	66	0.73	0.98	24	empty

Interfaces

1 interface between chains.

A–B · 1191 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5KSD · Crystal Structure of a Plasma Membrane Proton Pump · the same entry in another collection · chain A against A, TM-score 1.00
P19456 · AlphaFold monomer V2.0 prediction for ATPase 2, plasma membrane-type (P19456) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P19456
Elsewhere: RCSB PDB 5KSD · PDBe 5KSD · UniProt P19456

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