4GLS: D- Vascular endothelial growth factor-A
Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21. Determined by X-ray diffraction at 1.6 Å resolution. Released 5 Sept 2012.
- Method
- X-ray diffraction
- Resolution
- 1.6 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 6,092
- Mol. weight
- 73.49 kDa
- Released
- 5 Sept 2012
Explore 4GLS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4GLS contains 18 α-helices and 53 β-strands across 8 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.
Chain A: 2 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 1 |
| α-helix | 10-17 | 8 | |
| β-strand | 18 | 1 | 2 |
| β-strand | 20-27 | 8 | 3 |
| α-helix | 28-31 | 4 | |
| β-strand | 39-41 | 3 | 4 |
| β-strand | 44-51 | 8 | 3 |
| β-strand | 53 | 1 | 2 |
| β-strand | 57 | 1 | 4 |
| β-strand | 59-77 | 19 | 4 |
| β-strand | 81-99 | 19 | 4 |
Chain B: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 4 |
| α-helix | 10-17 | 8 | |
| β-strand | 18 | 1 | 5 |
| β-strand | 20-27 | 8 | 6 |
| α-helix | 28-31 | 4 | |
| β-strand | 39-41 | 3 | 1 |
| β-strand | 44-51 | 8 | 6 |
| β-strand | 53 | 1 | 5 |
| β-strand | 59-77 | 19 | 1 |
| β-strand | 81-99 | 19 | 1 |
Chain C: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 7 |
| β-strand | 12-17 | 6 | 7 |
| α-helix | 22-36 | 15 | |
| β-strand | 39-40 | 2 | 1 |
| β-strand | 42-46 | 5 | 7 |
| α-helix | 47-49 | 3 | |
| β-strand | 51-55 | 5 | 7 |
Chain D: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 8 |
| β-strand | 12-17 | 6 | 8 |
| α-helix | 22-36 | 15 | |
| β-strand | 39-40 | 2 | 9 |
| β-strand | 42-46 | 5 | 8 |
| β-strand | 51-55 | 5 | 8 |
Chains E and F: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7 | 1 | |
| β-strand | 8 | 1 | 9 |
| α-helix | 9 | 1 | |
| α-helix | 10-17 | 8 | |
| β-strand | 18 | 1 | 10 |
| β-strand | 20-27 | 8 | 11 |
| α-helix | 28-31 | 4 | |
| β-strand | 39-41 | 3 | 12 |
| β-strand | 44-51 | 8 | 11 |
| β-strand | 53 | 1 | 10 |
| β-strand | 59-77 | 19 | 12 |
| β-strand | 81-99 | 19 | 12 |
Chain G: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 16 |
| β-strand | 12-17 | 6 | 16 |
| α-helix | 22-34 | 13 | |
| β-strand | 39-40 | 2 | 4 |
| β-strand | 42-46 | 5 | 16 |
| β-strand | 51-55 | 5 | 16 |
Chain H: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 15 |
| β-strand | 12-17 | 6 | 15 |
| α-helix | 22-34 | 13 | |
| β-strand | 39-40 | 2 | 12 |
| β-strand | 42-46 | 5 | 15 |
| α-helix | 47-49 | 3 | |
| β-strand | 51-55 | 5 | 15 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| D- Vascular endothelial growth factor-A | A, B | protein | 102 | | |
| L- RFX001 | C, G | protein | 56 | | |
| D- RFX001 | D, H | protein | 56 | | |
| Vascular endothelial growth factor A | E, F | protein | 102 | Homo sapiens | P15692 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>4GLS_1 D- Vascular endothelial growth factor-A (chains A, B)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD
Sequence of entity 2 (C, G), FASTA
>4GLS_2 L- RFX001 (chains C, G)
TYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTFTVTE
Sequence of entity 3 (D, H), FASTA
>4GLS_3 D- RFX001 (chains D, H)
TYKLILNGKTLKGETTTEAVDVFDAFDVFFVYAASNFSDFDDWTYDDATKTFTVTE
Sequence of entity 4 (E, F), FASTA
>4GLS_4 Vascular endothelial growth factor A (chains E, F)
GQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLE
CVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD
Primary citation
Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography. Mandal, K., Uppalapati, M., Ault-Riche, D. et al. Proc Natl Acad Sci U S A (2012) 109:14779-14784. DOI 10.1073/pnas.1210483109 · PubMed
Other PDB entries of the same protein (UniProt P15692 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1MKK 1.32 Å, Disulfide deficient mutant of vascular endothelial growth factor A (C61A and C104A)
- 9JU1 1.45 Å, Helix-loop-helix peptide (VS42-LR3) in complex with VEGF-A
- 9KKU 1.46 Å, Helix-loop-helix peptide (M49) in complex with VEGF-A
- 4GLN 1.6 Å, Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus…
- 6ZBR 1.6 Å, VEGF-A 13:107 crystallized with 4C bicyclic peptide
- 6ZFL 1.6 Å, High resolution structure of VEGF-A 12:107 crystallized in tetragonal form
- 1FLT 1.7 Å, Vegf in complex with domain 2 of the flt-1 receptor
- 4KZN 1.71 Å, crystal structure of human VEGF-A receptor binding domain
- 4QAF 1.8 Å, Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109)
- 6Z13 1.8 Å, VEGF-A 13:107 crystallized with 3C bicyclic peptide
- 6ZCD 1.8 Å, VEGF-A 13:107 crystallized with 1C bicyclic peptide
- 3QTK 1.85 Å, The crystal structure of chemically synthesized VEGF-A
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