MolNFT v1 · #113301 · protein
Crystal structure of vegfr-1 domain 2 in presence of cu
5ABD · Vascular endothelial growth factor receptor 1: “Crystal structure of vegfr-1 domain 2 in presence of cu”. X-ray diffraction, 3 ligands (CU, NA, SO4), 2 pockets (best druggability 0.67). MolNFT v1 #113301 on GenesisL1: 3D structure…
- PDB
- 5ABD
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor receptor 1
- EC
- 2.7.10.1
- UniProt
- P17948
- Ligands
- CU, NA, SO4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, X | Vascular endothelial growth factor receptor 1 (EC 2.7.10.1) | protein | 95 | 3% helix, 48% strand | P17948 |
| I | Vascular endothelial growth factor receptor 1 (EC 2.7.10.1) | protein | 93 | 3% helix, 46% strand | P17948 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 5 copies · chains I, E, X
- NA · Sodium ion · metal · 2 copies · chains E, X
- SO4 · Sulfate ion · ion · 2 copies · chains E, I, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.67 | 0.76 | 51 | SO4 |
| 2 | 150 | 0.43 | 0.74 | 30 | empty |
Interfaces
3 interfaces between chains.
- E–X · 497 Ų buried · 1 hydrogen bond · protein-protein
- E–I · 365 Ų buried · 0 hydrogen bonds · protein-protein
- I–X · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5ABD · Crystal structure of vegfr-1 domain 2 in presence of cu · the same entry in another collection · chain E against E, TM-score 1.00
- P17948 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 1… · a predicted model of the same protein · chain I against A, TM-score 0.97
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 P17948
- Elsewhere: RCSB PDB 5ABD · PDBe 5ABD · UniProt P17948
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