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X-ray structure of FE(II)-soaked unda bound to lauric acid

Analyse X-ray structure of FE(II)-soaked unda bound to lauric acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P5Q
Type: protein
Length: 491 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Unda
Ligands: DAO, FE
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Unda	protein	252	77% helix, 0% strand	—
B	Unda	protein	239	78% helix, 0% strand	—

Ligands and binding sites

DAO · Lauric acid · ligand · 2 copies · chains A, B
FE · Fe (III) ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	151	0.79	0.95	31	DAO, FE
2	120	0.78	0.96	22	DAO
3	349	0.59	0.77	29	empty
4	326	0.57	0.76	29	empty
5	108	0.37	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 815 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6P5Q · X-ray structure of Fe(II)-soaked UndA bound to lauric acid · the same entry in another collection · 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
Elsewhere: RCSB PDB 6P5Q · PDBe 6P5Q

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