MolNFT v1 · #59411 · protein

Engineered human lipocalin 2 (LCN2), apo-form

3BX8: “Engineered human lipocalin 2 (LCN2), apo-form”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #59411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BX8
Type: protein
Length: 1,310 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Engineered human lipocalin 2
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 13% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Engineered human lipocalin 2	protein	167	14% helix, 41% strand	—
B	Engineered human lipocalin 2	protein	166	14% helix, 41% strand	—
D	Engineered human lipocalin 2	protein	168	14% helix, 42% strand	—
E	Engineered human lipocalin 2	protein	162	12% helix, 41% strand	—
F	Engineered human lipocalin 2	protein	158	14% helix, 41% strand	—
G	Engineered human lipocalin 2	protein	161	14% helix, 41% strand	—
H	Engineered human lipocalin 2	protein	161	12% helix, 43% strand	—

Ligands and binding sites

PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 5 copies · chains B, C, D, F, H
1PE · Pentaethylene glycol · additive · 3 copies · chains A, E, G

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

Pockets

20 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	933	0.79	0.81	79	empty
2	1038	0.78	0.80	93	empty
3	492	0.67	0.78	49	empty
4	208	0.50	0.75	25	PE5
5	195	0.49	0.76	27	PE5

Interfaces

13 interfaces between chains.

B–F · 661 Å² buried · 10 hydrogen bonds · protein-protein
C–E · 653 Å² buried · 15 hydrogen bonds · protein-protein
D–G · 652 Å² buried · 11 hydrogen bonds · protein-protein
A–F · 413 Å² buried · 2 hydrogen bonds · protein-protein
C–G · 412 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3BX8 · Engineered Human Lipocalin 2 (LCN2), apo-form · 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 3BX8 · PDBe 3BX8

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