MolNFT v1 · #104438 · protein

Crystal structure of an engineered lipocalin (anticalin) in complex with human hepcidin

4QAE: “Crystal structure of an engineered lipocalin (anticalin) in complex with human hepcidin”. X-ray diffraction, 1 ligand (CL), 13 pockets (best druggability 0.84). MolNFT v1 #104438 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4QAE
Type: protein
Length: 1,149 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hepcidin; Neutrophil gelatinase-associated lipocalin
UniProt: P81172, P80188
Ligands: CL
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 8 distinct chains · 13% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P, U	Hepcidin	protein	25	0% helix, 40% strand	P81172
Q, R, S	Hepcidin	protein	24	0% helix, 42% strand	P81172
T	Hepcidin	protein	23	0% helix, 43% strand	P81172
A	Neutrophil gelatinase-associated lipocalin	protein	172	13% helix, 42% strand	P80188
B	Neutrophil gelatinase-associated lipocalin	protein	175	13% helix, 41% strand	P80188
C	Neutrophil gelatinase-associated lipocalin	protein	163	14% helix, 44% strand	P80188
D, F	Neutrophil gelatinase-associated lipocalin	protein	164	14% helix, 43% strand	P80188
E	Neutrophil gelatinase-associated lipocalin	protein	166	14% helix, 43% strand	P80188

Ligands and binding sites

CL · Chloride ion · ion · 5 copies · chains B, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains R, A, D, P, B, E, T, U, Q, C, F, S

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	580	0.84	0.89	109	MPD
2	410	0.78	0.87	59	MPD
3	273	0.77	0.89	43	empty
4	547	0.69	0.79	55	empty
5	618	0.68	0.77	59	empty

Interfaces

30 interfaces between chains.

P–A · 883 Å² buried · 9 hydrogen bonds · protein-protein
T–E · 878 Å² buried · 8 hydrogen bonds · protein-protein
U–F · 862 Å² buried · 7 hydrogen bonds · protein-protein
Q–B · 854 Å² buried · 8 hydrogen bonds · protein-protein
S–D · 834 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 disulfide (disulfide).

Compared structures

4QAE · Crystal structure of an engineered lipocalin (Anticalin) in complex with human hepcidin · the same entry in another collection · chain F against F, 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 P81172
Every structure of UniProt P80188
Elsewhere: RCSB PDB 4QAE · PDBe 4QAE · UniProt P81172 · UniProt P80188

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