Research workbench
Structure of zebov gp in complex with 5T0180 antibody
Analyse Structure of zebov gp in complex with 5T0180 antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S8J
- Type
- protein
- Length
- 1,584 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain; Envelope glycoprotein 1; Envelope glycoprotein
- UniProt
- A0A0U3BWW0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, O, U | Light chain | protein | 110 | 3% helix, 46% strand | — |
| H, P, Y | Heavy chain | protein | 122 | 5% helix, 44% strand | — |
| A, C, E | Envelope glycoprotein 1 | protein | 186 | 6% helix, 42% strand | — |
| B, D, F | Envelope glycoprotein | protein | 110 | 38% helix, 15% strand | A0A0U3BWW0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, F, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.81 | 0.83 | 107 | empty |
| 2 | 557 | 0.78 | 0.84 | 61 | empty |
| 3 | 552 | 0.77 | 0.84 | 60 | empty |
| 4 | 564 | 0.76 | 0.83 | 61 | empty |
| 5 | 166 | 0.67 | 0.87 | 34 | empty |
Interfaces
30 interfaces between chains.
- A–B · 2689 Ų buried · 24 hydrogen bonds · protein-protein
- F–E · 2658 Ų buried · 26 hydrogen bonds · protein-protein
- D–C · 2655 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1104 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1079 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6S8J · Structure of ZEBOV GP in complex with 5T0180 antibody · the same entry in another collection · chain L against L, 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 A0A0U3BWW0
- Elsewhere: RCSB PDB 6S8J · PDBe 6S8J · UniProt A0A0U3BWW0
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