MolNFT v1 · #139192 · protein

Crystal structure of the dog lipocalin allergen can F 6

5X7Y · Lipocalin-can F 6 allergen: “Crystal structure of the dog lipocalin allergen can F 6”. X-ray diffraction, 9 pockets (best druggability 0.79). MolNFT v1 #139192 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X7Y
Type: protein
Length: 637 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipocalin-can F 6 allergen
UniProt: H2B3G5
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipocalin-can F 6 allergen	protein	159	17% helix, 45% strand	H2B3G5
B	Lipocalin-can F 6 allergen	protein	161	14% helix, 45% strand	H2B3G5
C	Lipocalin-can F 6 allergen	protein	160	16% helix, 46% strand	H2B3G5
D	Lipocalin-can F 6 allergen	protein	157	15% helix, 47% strand	H2B3G5

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.79	0.99	16	PEG
2	88	0.77	0.98	18	PEG
3	80	0.77	0.98	17	PEG
4	381	0.76	0.86	65	empty
5	71	0.75	0.98	16	PEG

Interfaces

4 interfaces between chains.

B–D · 906 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 881 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 490 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 30 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5X7Y · Crystal Structure of the Dog Lipocalin Allergen Can f 6 · the same entry in another collection · chain D against D, TM-score 1.00
H2B3G5 · AlphaFold monomer V2.0 prediction for lipocalin can F 6.0101 (H2B3G5) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 H2B3G5
Elsewhere: RCSB PDB 5X7Y · PDBe 5X7Y · UniProt H2B3G5

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