Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109). Determined by X-ray diffraction at 1.8 Å resolution. Released 6 May 2015.
Explore 4QAF in 3D Show helices and sheets RCSB PDB PDBe
4QAF contains 11 α-helices and 37 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 15-17 | 3 | 1 |
| β-strand | 18-22 | 5 | 2 |
| β-strand | 31-36 | 6 | 1 |
| β-strand | 40-43 | 4 | 2 |
| α-helix | 44 | 1 | |
| β-strand | 49-55 | 7 | 2 |
| β-strand | 62-69 | 8 | 2 |
| α-helix | 82 | 1 | |
| β-strand | 83-87 | 5 | 1 |
| β-strand | 97-101 | 5 | 1 |
| α-helix | 102-104 | 3 | |
| β-strand | 105 | 1 | 3 |
| β-strand | 110 | 1 | 3 |
| β-strand | 112-115 | 4 | 1 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 15-17 | 3 | 9 |
| β-strand | 18-22 | 5 | 10 |
| β-strand | 31-36 | 6 | 9 |
| β-strand | 40-42 | 3 | 10 |
| β-strand | 49-53 | 5 | 10 |
| β-strand | 64-69 | 6 | 10 |
| β-strand | 83-87 | 5 | 9 |
| β-strand | 97-101 | 5 | 9 |
| α-helix | 102-104 | 3 | |
| β-strand | 110 | 1 | 6 |
| β-strand | 112-115 | 4 | 9 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 14 | 1 | |
| β-strand | 15 | 1 | 3 |
| α-helix | 16 | 1 | |
| α-helix | 17-24 | 8 | |
| β-strand | 25 | 1 | 4 |
| β-strand | 27-34 | 8 | 5 |
| α-helix | 35-38 | 4 | |
| α-helix | 40-42 | 3 | |
| β-strand | 46-48 | 3 | 6 |
| β-strand | 51-58 | 8 | 5 |
| β-strand | 60 | 1 | 4 |
| β-strand | 66-84 | 19 | 6 |
| β-strand | 88-106 | 19 | 6 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 15 | 1 | 6 |
| α-helix | 17-24 | 8 | |
| β-strand | 25 | 1 | 7 |
| β-strand | 27-34 | 8 | 8 |
| α-helix | 35-38 | 4 | |
| β-strand | 46-48 | 3 | 3 |
| β-strand | 51-58 | 8 | 8 |
| β-strand | 60 | 1 | 7 |
| β-strand | 67-84 | 18 | 3 |
| β-strand | 88-105 | 18 | 3 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Lipocalin-1 | A, B | protein | 152 | Homo sapiens | P31025 (AlphaFold model) |
| Vascular endothelial growth factor A | C, D | protein | 112 | Homo sapiens | P15692 (AlphaFold model) |
>4QAF_1 Lipocalin-1 (chains A, B) ASDEEIQDVSGTWYLKAMTVDVGALRCLAGSVIPTTLTTLEGGNLEAKVTMHIKGRSQEV KAVLSKTDEPGIYTAIGGIHVAKIGRSHVKDHYIFYSEGCLSGVPVPGVWLVGRDPKNNL EALEDFEKAAGARGLSTESILIPRQSETSSPG
>4QAF_2 Vascular endothelial growth factor A (chains C, D) GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKDSAWSHPQFEK
| ID | Name | Formula | Copies |
|---|---|---|---|
| OMA | 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid | C19 H34 O2 | 2 |
Water and common crystallization additives (SO4, ACT) are not listed.
Crystal structure of an Anticalin with specific blocking activity towards human vascular endothelial growth factor (VEGF) reveals plasticity of the lipocalin fold. Giese, T., Skerra, A. To be published.
Other PDB entries of the same protein (UniProt P31025 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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