MolNFT v1 · #169776 · protein

Structure of P5A-ATPase SPF1, AMP-pcp-bound form

6XMQ · P5A-type ATPase: “Structure of P5A-ATPase SPF1, AMP-pcp-bound form”. Electron microscopy, 2 ligands (ACP, MG), 17 pockets (best druggability 0.83). MolNFT v1 #169776 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XMQ
Type: protein
Length: 1,085 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: ACP, MG
Pockets: 17 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	P5A-type ATPase (EC 7.2.2.-)	protein	1085	43% helix, 17% strand	P39986

Ligands and binding sites

ACP · Phosphomethylphosphonic acid adenylate ester · 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

17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1147	0.83	0.84	105	empty
2	1198	0.82	0.83	107	ACP
3	74	0.69	0.95	23	empty
4	345	0.61	0.77	40	empty
5	169	0.55	0.80	27	empty

Compared structures

6XMQ · Structure of P5A-ATPase Spf1, AMP-PCP-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 0.91

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 6XMQ · PDBe 6XMQ · UniProt P39986

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