Research workbench
Crystal structure of chemically synthesized heterochiral {D-protein antagonist plus VEGF-a} protein complex in space group P21/N
Analyse Crystal structure of chemically synthesized heterochiral {D-protein antagonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GLN
- Type
- protein
- Length
- 302 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-RFX001; Vascular endothelial growth factor a
- UniProt
- P15692
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, H | D-RFX001 | protein | 56 | 27% helix, 43% strand | — |
| E, F | Vascular endothelial growth factor a | protein | 95 | 13% helix, 63% strand | P15692 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.45 | 0.77 | 32 | empty |
| 2 | 107 | 0.40 | 0.76 | 32 | empty |
| 3 | 58 | 0.25 | 0.72 | 20 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1346 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 385 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 383 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 367 Ų buried · 4 hydrogen bonds · protein-protein
- F–H · 361 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 108 d-amino, 8 disulfide (D-amino acid, disulfide).
Compared structures
- 4GLN · Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus… · the same entry in another collection · chain D against D, 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 P15692
- Elsewhere: RCSB PDB 4GLN · PDBe 4GLN · UniProt P15692
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