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Crystal structure of vsv-indiana (mudd-summers strain) glycoprotein under its acidic conformation
Analyse Crystal structure of vsv-indiana (mudd-summers strain) glycoprotein under its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I2M
- Type
- protein
- Length
- 1,227 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G
- UniProt
- P0C2X0
- Ligands
- CA
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein G | protein | 409 | 22% helix, 38% strand | P0C2X0 |
| B | Glycoprotein G | protein | 410 | 22% helix, 39% strand | P0C2X0 |
| C | Glycoprotein G | protein | 408 | 22% helix, 39% strand | P0C2X0 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.88 | 0.89 | 83 | empty |
| 2 | 1068 | 0.79 | 0.81 | 113 | PE4 |
| 3 | 731 | 0.73 | 0.79 | 91 | empty |
| 4 | 649 | 0.72 | 0.79 | 78 | empty |
| 5 | 449 | 0.71 | 0.81 | 56 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2128 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 2055 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1943 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5I2M · Crystal structure of vsv-indiana (mudd-summers strain) glycoprotein under its acidic… · the same entry in another collection · chain A against A, 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 P0C2X0
- Elsewhere: RCSB PDB 5I2M · PDBe 5I2M · UniProt P0C2X0
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