Research workbench
Crystal structure of the SARS-cov-2 receptor binding domain in complex with CR3022 Fab (crystal form 1)
Analyse Crystal structure of the SARS-cov-2 receptor binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YM0
- Type
- protein
- Length
- 634 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain; Light chain
- UniProt
- P0DTC2
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike glycoprotein | protein | 197 | 13% helix, 30% strand | P0DTC2 |
| H | Heavy chain | protein | 217 | 6% helix, 53% strand | — |
| L | Light chain | protein | 220 | 6% helix, 52% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.55 | 0.75 | 43 | empty |
| 2 | 132 | 0.51 | 0.80 | 26 | empty |
| 3 | 68 | 0.35 | 0.77 | 20 | empty |
| 4 | 63 | 0.35 | 0.78 | 19 | empty |
| 5 | 65 | 0.35 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1981 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 654 Ų buried · 12 hydrogen bonds · protein-protein
- E–L · 442 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6YM0 · Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab… · the same entry in another collection · chain E against E, 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 P0DTC2
- Elsewhere: RCSB PDB 6YM0 · PDBe 6YM0 · UniProt P0DTC2
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