MolNFT v1 · #115224 · protein

Crystal structure of the ntd of drosophila oskar protein

5CD8 · Maternal effect protein oskar: “Crystal structure of the ntd of drosophila oskar protein”. X-ray diffraction, 4 pockets (best druggability 0.79). MolNFT v1 #115224 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CD8
Type: protein
Length: 440 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maternal effect protein oskar
UniProt: P25158
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maternal effect protein oskar	protein	76	41% helix, 14% strand	P25158
B, C	Maternal effect protein oskar	protein	74	43% helix, 12% strand	P25158
D, F	Maternal effect protein oskar	protein	73	42% helix, 12% strand	P25158
E	Maternal effect protein oskar	protein	70	43% helix, 16% strand	P25158

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, E, B, C, D

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

Pockets

4 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	962	0.79	0.81	86	GOL
2	210	0.54	0.78	22	empty
3	103	0.38	0.76	16	empty
4	71	0.30	0.74	20	empty

Interfaces

10 interfaces between chains.

E–F · 691 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 627 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 592 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 355 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 230 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5CD8 · Crystal structure of the NTD of Drosophila Oskar protein · the same entry in another collection · chain F against F, TM-score 1.00
P25158 · AlphaFold monomer V2.0 prediction for maternal effect protein oskar (P25158) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P25158
Elsewhere: RCSB PDB 5CD8 · PDBe 5CD8 · UniProt P25158

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