Research workbench
Crystal structure of host-primed ebola virus gp, gpcl.
Analyse Crystal structure of host-primed ebola virus gp, gpcl. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HJ3
- Type
- protein
- Length
- 2,680 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein; KZ52 antibody fragment
- UniProt
- Q05320, P87666
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 12 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Envelope glycoprotein | protein | 159 | 8% helix, 43% strand | Q05320 |
| D, H, L, P | Envelope glycoprotein | protein | 110 | 35% helix, 11% strand | P87666 |
| E | KZ52 antibody fragment | protein | 204 | 4% helix, 51% strand | — |
| F | KZ52 antibody fragment | protein | 189 | 2% helix, 49% strand | — |
| G | Envelope glycoprotein | protein | 158 | 8% helix, 43% strand | Q05320 |
| I | KZ52 antibody fragment | protein | 199 | 5% helix, 51% strand | — |
| J | KZ52 antibody fragment | protein | 209 | 4% helix, 46% strand | — |
| K, O | Envelope glycoprotein | protein | 157 | 8% helix, 44% strand | Q05320 |
| M | KZ52 antibody fragment | protein | 203 | 6% helix, 48% strand | — |
| N | KZ52 antibody fragment | protein | 203 | 4% helix, 50% strand | — |
| A | KZ52 antibody fragment | protein | 199 | 5% helix, 49% strand | — |
| B | KZ52 antibody fragment | protein | 203 | 4% helix, 46% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains J, P, F, H, K, N, L, O, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, D, G, H, P, K, L, O
- BMA · beta-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.88 | 0.89 | 102 | empty |
| 2 | 57 | 0.71 | 0.98 | 19 | empty |
| 3 | 64 | 0.70 | 0.97 | 22 | empty |
| 4 | 55 | 0.70 | 0.98 | 22 | empty |
| 5 | 131 | 0.68 | 0.89 | 23 | empty |
Interfaces
34 interfaces between chains.
- G–H · 2551 Ų buried · 32 hydrogen bonds · protein-protein
- O–P · 2537 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2537 Ų buried · 33 hydrogen bonds · protein-protein
- K–L · 2526 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 1753 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5HJ3 · Crystal structure of host-primed Ebola virus GP, GPcl. · the same entry in another collection · chain C against C, 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 Q05320
- Every structure of UniProt P87666
- Elsewhere: RCSB PDB 5HJ3 · PDBe 5HJ3 · UniProt Q05320 · UniProt P87666
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