Research workbench
MERS-cov complex with human neutralizing LCA60 antibody Fab fragment (state 1)
Analyse MERS-cov complex with human neutralizing LCA60 antibody Fab fragment (state 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NB3
- Type
- protein
- Length
- 3,757 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; LCA60 light chain; LCA60 heavy chain
- UniProt
- A0A140AYW5
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1169 | 19% helix, 32% strand | A0A140AYW5 |
| L, E | LCA60 light chain | protein | 107 | 7% helix, 44% strand | — |
| H | LCA60 heavy chain | protein | 124 | 7% helix, 52% strand | — |
| D | LCA60 heavy chain | protein | 123 | 10% helix, 50% strand | — |
| B | Spike glycoprotein | protein | 958 | 22% helix, 33% strand | A0A140AYW5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, C, H, B, D
- MAN · alpha-D-mannopyranose · sugar · 37 copies · chains L, H, A, C, B, D, E
- BMA · beta-D-mannopyranose · sugar · 30 copies · chains A, H, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.85 | 0.87 | 99 | empty |
| 2 | 697 | 0.85 | 0.88 | 91 | empty |
| 3 | 824 | 0.84 | 0.87 | 88 | empty |
| 4 | 900 | 0.84 | 0.86 | 113 | empty |
| 5 | 731 | 0.82 | 0.86 | 82 | empty |
Interfaces
11 interfaces between chains.
- A–C · 5548 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 5029 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 4245 Ų buried · 51 hydrogen bonds · protein-protein
- D–E · 873 Ų buried · 9 hydrogen bonds · protein-protein
- L–H · 865 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 49 glycan (disulfide, N-glycosylation).
Compared structures
- 6NB3 · MERS-CoV complex with human neutralizing LCA60 antibody Fab fragment (state 1) · 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 A0A140AYW5
- Elsewhere: RCSB PDB 6NB3 · PDBe 6NB3 · UniProt A0A140AYW5
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