MolNFT v1 · #168268 · protein
Crystal structure of the SARS-cov-1 rbd bound by the cross-reactive single-domain antibody SARS vhh-72
6WAQ · Nanobody SARS vhh-72: “Crystal structure of the SARS-cov-1 rbd bound by the cross-reactive single-domain antibody SARS vhh-72”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.60). MolNFT v1 #168268 on GenesisL1…
- PDB
- 6WAQ
- Type
- protein
- Length
- 626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody SARS vhh-72; Spike glycoprotein
- UniProt
- P59594
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody SARS vhh-72 | protein | 127 | 9% helix, 51% strand | — |
| D | Spike glycoprotein | protein | 184 | 20% helix, 27% strand | P59594 |
| C | Nanobody SARS vhh-72 | protein | 125 | 10% helix, 52% strand | — |
| B | Spike glycoprotein | protein | 190 | 17% helix, 26% strand | P59594 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.60 | 0.77 | 51 | empty |
| 2 | 210 | 0.52 | 0.77 | 32 | empty |
| 3 | 70 | 0.44 | 0.81 | 16 | empty |
| 4 | 138 | 0.40 | 0.74 | 22 | empty |
| 5 | 126 | 0.38 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- D–C · 864 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 839 Ų buried · 16 hydrogen bonds · protein-protein
- D–B · 679 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6WAQ · Crystal structure of the SARS-CoV-1 RBD bound by the cross-reactive single-domain… · the same entry in another collection · chain B against B, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against E, TM-score 0.91
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against E, TM-score 0.91
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against E, TM-score 0.90
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against E, TM-score 0.90
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against E, TM-score 0.90
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against E, TM-score 0.90
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 P59594
- Elsewhere: RCSB PDB 6WAQ · PDBe 6WAQ · UniProt P59594
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