Research workbench
Crystal structure of the MERS-cov rbd bound by the neutralizing single-domain antibody MERS vhh-55
Analyse Crystal structure of the MERS-cov rbd bound by the neutralizing single-domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WAR
- Type
- protein
- Length
- 2,647 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein; Nanobody MERS vhh-55
- UniProt
- A0A0U2MS80
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, M, O | Spike protein | protein | 211 | 14% helix, 36% strand | A0A0U2MS80 |
| B | Nanobody MERS vhh-55 | protein | 121 | 2% helix, 50% strand | — |
| D | Nanobody MERS vhh-55 | protein | 124 | 5% helix, 52% strand | — |
| F, H, J, N, P | Nanobody MERS vhh-55 | protein | 120 | 5% helix, 53% strand | — |
| K | Spike protein | protein | 210 | 14% helix, 36% strand | A0A0U2MS80 |
| L | Nanobody MERS vhh-55 | protein | 115 | 5% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, J, G, O
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 | 1116 | 0.79 | 0.81 | 135 | empty |
| 2 | 1181 | 0.79 | 0.80 | 108 | empty |
| 3 | 640 | 0.76 | 0.82 | 65 | empty |
| 4 | 957 | 0.75 | 0.78 | 103 | empty |
| 5 | 715 | 0.73 | 0.79 | 74 | empty |
Interfaces
35 interfaces between chains.
- C–G · 912 Ų buried · 14 hydrogen bonds · protein-protein
- A–K · 835 Ų buried · 8 hydrogen bonds · protein-protein
- K–L · 748 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 731 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 725 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 4 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 6WAR · Crystal structure of the MERS-CoV RBD bound by the neutralizing single-domain antibody… · 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 A0A0U2MS80
- Elsewhere: RCSB PDB 6WAR · PDBe 6WAR · UniProt A0A0U2MS80
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