MolNFT v1 · #169779 · protein

Structure of P5A-ATPase SPF1, BEF3-bound form

6XMT · P5A-type ATPase: “Structure of P5A-ATPase SPF1, BEF3-bound form”. Electron microscopy, 2 ligands (BEF, MG), 20 pockets (best druggability 0.78). MolNFT v1 #169779 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XMT
Type: protein
Length: 1,092 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P5A-type ATPase
EC: 7.2.2.-
UniProt: P39986
Ligands: BEF, MG
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · 1 distinct chain · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	P5A-type ATPase (EC 7.2.2.-)	protein	1092	41% helix, 16% strand	P39986

Ligands and binding sites

BEF · Beryllium trifluoride ion · ligand · chains A
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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1090	0.78	0.80	81	empty
2	486	0.75	0.83	56	empty
3	681	0.70	0.77	51	empty
4	510	0.66	0.77	61	empty
5	171	0.64	0.85	24	empty

Compared structures

6XMT · Structure of P5A-ATPase Spf1, BeF3-bound form · the same entry in another collection · chain A against A, TM-score 1.00
P39986 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum transmembrane helix… · a predicted model of the same protein · chain A against A, TM-score 0.79

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 P39986
Elsewhere: RCSB PDB 6XMT · PDBe 6XMT · UniProt P39986

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