MolNFT v1 · #136375 · protein
Crystal structure of marburg virus gp in complex with the human survivor antibody MR78
5UQY · Envelope glycoprotein GP1: “Crystal structure of marburg virus gp in complex with the human survivor antibody MR78”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.76). MolNFT v1 #136375 on GenesisL1…
- 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.