Research workbench
Crystal structure of an engineered lipocalin (anticalin) in complex with human hepcidin
Analyse Crystal structure of an engineered lipocalin (anticalin) in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 9 hydrogen bonds · protein-protein
- T–E · 878 Ų buried · 8 hydrogen bonds · protein-protein
- U–F · 862 Ų buried · 7 hydrogen bonds · protein-protein
- Q–B · 854 Ų buried · 8 hydrogen bonds · protein-protein
- S–D · 834 Ų 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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