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Complex structure of OSYCHF1 with gmp-pnp

Analyse Complex structure of OSYCHF1 with gmp-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EE9
Type: protein
Length: 716 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Obg-like ATPase 1
EC: 3.6.5.-
UniProt: Q6Z1J6
Ligands: GNP, MG, K
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Obg-like ATPase 1 (EC 3.6.5.-)	protein	357	43% helix, 19% strand	Q6Z1J6
B	Obg-like ATPase 1 (EC 3.6.5.-)	protein	359	45% helix, 19% strand	Q6Z1J6

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A
K · Potassium ion · metal · chains B
GOL · Glycerol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	161	0.75	0.92	30	empty
2	75	0.60	0.89	24	empty
3	214	0.49	0.75	31	empty
4	153	0.43	0.75	19	empty
5	94	0.41	0.77	21	empty

Compared structures

5EE9 · Complex structure of OSYCHF1 with GMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
Q6Z1J6 · AlphaFold monomer V2.0 prediction for obg-like ATPase 1 (Q6Z1J6) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q6Z1J6
Elsewhere: RCSB PDB 5EE9 · PDBe 5EE9 · UniProt Q6Z1J6

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