Research workbench
Crystal structure of marburg virus gp in complex with the human survivor antibody MR78
Analyse Crystal structure of marburg virus gp in complex with the human survivor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UQY
- Type
- protein
- Length
- 2,694 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP1; Envelope glycoprotein GP2; MR78 Fab light chain; MR78 Fab…
- UniProt
- Q1PDC7
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 12 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP1 | protein | 145 | 9% helix, 42% strand | Q1PDC7 |
| B | Envelope glycoprotein GP2 | protein | 127 | 31% helix, 12% strand | Q1PDC7 |
| C, G, K, O | MR78 Fab light chain | protein | 210 | 7% helix, 50% strand | — |
| D | MR78 Fab heavy chain | protein | 218 | 6% helix, 53% strand | — |
| E | Envelope glycoprotein GP1 | protein | 144 | 8% helix, 42% strand | Q1PDC7 |
| F | Envelope glycoprotein GP2 | protein | 94 | 36% helix, 17% strand | Q1PDC7 |
| H | MR78 Fab heavy chain | protein | 220 | 6% helix, 54% strand | — |
| I, M | Envelope glycoprotein GP1 | protein | 142 | 8% helix, 43% strand | Q1PDC7 |
| J | Envelope glycoprotein GP2 | protein | 97 | 35% helix, 13% strand | Q1PDC7 |
| L | MR78 Fab heavy chain | protein | 222 | 6% helix, 53% strand | — |
| N | Envelope glycoprotein GP2 | protein | 92 | 37% helix, 16% strand | Q1PDC7 |
| P | MR78 Fab heavy chain | protein | 211 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, E, F, J, I, N, M
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, C, E, J, F, M
- BMA · beta-D-mannopyranose · sugar · 5 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.76 | 0.78 | 95 | empty |
| 2 | 527 | 0.73 | 0.81 | 66 | empty |
| 3 | 433 | 0.72 | 0.82 | 34 | empty |
| 4 | 471 | 0.71 | 0.81 | 59 | empty |
| 5 | 403 | 0.69 | 0.81 | 53 | empty |
Interfaces
33 interfaces between chains.
- A–B · 2522 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2383 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 2347 Ų buried · 20 hydrogen bonds · protein-protein
- M–N · 2293 Ų buried · 26 hydrogen bonds · protein-protein
- K–L · 1919 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5UQY · Crystal structure of Marburg virus GP in complex with the human survivor antibody MR78 · 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 Q1PDC7
- Elsewhere: RCSB PDB 5UQY · PDBe 5UQY · UniProt Q1PDC7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.