Research workbench
Crystal structure of the SARS-cov-2 S rbd in complex with bd-515 Fab
Analyse Crystal structure of the SARS-cov-2 S rbd in complex with bd-515 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E88
- Type
- protein
- Length
- 2,446 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bd-515 Fab heavy chain; Bd-515 Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bd-515 Fab heavy chain | protein | 213 | 10% helix, 52% strand | — |
| B, E, H, K | Bd-515 Fab light chain | protein | 212 | 5% helix, 53% strand | — |
| C, I, L | Spike protein S1 | protein | 189 | 14% helix, 27% strand | P0DTC2 |
| D, G | Bd-515 Fab heavy chain | protein | 210 | 7% helix, 54% strand | — |
| F | Spike protein S1 | protein | 188 | 13% helix, 31% strand | P0DTC2 |
| J | Bd-515 Fab heavy chain | protein | 210 | 7% helix, 53% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.77 | 0.79 | 99 | empty |
| 2 | 537 | 0.64 | 0.76 | 57 | empty |
| 3 | 391 | 0.64 | 0.79 | 50 | empty |
| 4 | 312 | 0.63 | 0.80 | 33 | empty |
| 5 | 581 | 0.62 | 0.74 | 62 | empty |
Interfaces
20 interfaces between chains.
- D–E · 1734 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1722 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1682 Ų buried · 15 hydrogen bonds · protein-protein
- J–K · 1670 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 775 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 7E88 · Crystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab · 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 P0DTC2
- Elsewhere: RCSB PDB 7E88 · PDBe 7E88 · UniProt P0DTC2
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