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Crystal structure of olfactomedin domain from gliomedin

Analyse Crystal structure of olfactomedin domain from gliomedin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XAV
Type: protein
Length: 976 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gliomedin
UniProt: Q8BMF8
Ligands: NA, PO4
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Gliomedin	protein	244	5% helix, 54% strand	Q8BMF8

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 8 copies · chains A, C, D, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	734	0.77	0.81	72	empty
2	529	0.72	0.81	64	GOL, PO4
3	144	0.53	0.80	24	empty
4	125	0.45	0.78	25	PO4
5	164	0.45	0.75	27	PO4

Interfaces

5 interfaces between chains.

A–C · 444 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 436 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 285 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 208 Å² buried · 1 hydrogen bond · protein-protein
A–B · 112 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4XAV · Crystal structure of olfactomedin domain from gliomedin · the same entry in another collection · chain D against D, TM-score 1.00
Q8BMF8 · AlphaFold monomer V2.0 prediction for gliomedin (Q8BMF8) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q8BMF8
Elsewhere: RCSB PDB 4XAV · PDBe 4XAV · UniProt Q8BMF8

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