MolNFT v1 · #127694 · protein

Structure of anticalin N7E in complex with the three-domain fragment FN7B8 of human oncofetal fibronectin

5N47 · Neutrophil gelatinase-associated lipocalin: “Structure of anticalin N7E in complex with the three-domain fragment FN7B8 of human oncofetal fibronectin”. X-ray diffraction, 11 pockets (best druggability 0.79). MolNFT v1 #127694 on…

PDB: 5N47
Type: protein
Length: 1,268 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neutrophil gelatinase-associated lipocalin; Fibronectin
UniProt: P80188, P02751
Pockets: 11 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neutrophil gelatinase-associated lipocalin	protein	180	13% helix, 40% strand	P80188
B	Fibronectin	protein	183	0% helix, 51% strand	P02751
C	Neutrophil gelatinase-associated lipocalin	protein	176	13% helix, 42% strand	P80188
D	Fibronectin	protein	280	1% helix, 52% strand	P02751
E	Neutrophil gelatinase-associated lipocalin	protein	172	13% helix, 42% strand	P80188
F	Fibronectin	protein	277	0% helix, 53% strand	P02751

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	974	0.79	0.81	83	empty
2	601	0.74	0.81	51	empty
3	581	0.71	0.79	48	empty
4	281	0.57	0.77	41	empty
5	131	0.54	0.81	23	empty

Interfaces

7 interfaces between chains.

C–D · 1395 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1318 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1240 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 682 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 471 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5N47 · Structure of Anticalin N7E in complex with the three-domain fragment Fn7B8 of human… · the same entry in another collection · chain F against F, TM-score 1.00
P02751 · AlphaFold monomer V2.0 prediction for fibronectin (P02751) · a predicted model of the same protein · chain B against A, TM-score 0.70

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 P80188
Every structure of UniProt P02751
Elsewhere: RCSB PDB 5N47 · PDBe 5N47 · UniProt P80188 · UniProt P02751

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