MolNFT v1 · #177116 · protein
Crystal structure of the SARS-cov-2 S rbd in complex with bd-623 Fab
7E7Y · Bd-623 Fab H: “Crystal structure of the SARS-cov-2 S rbd in complex with bd-623 Fab”. X-ray diffraction, 6 pockets (best druggability 0.58). MolNFT v1 #177116 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E7Y
- Type
- protein
- Length
- 1,235 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bd-623 Fab H; Bd-623 Fab L; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bd-623 Fab H | protein | 218 | 12% helix, 51% strand | — |
| B, D | Bd-623 Fab L | protein | 209 | 7% helix, 50% strand | — |
| R | Spike protein S1 | protein | 189 | 18% helix, 29% strand | P0DTC2 |
| C | Bd-623 Fab H | protein | 216 | 12% helix, 52% strand | — |
| E | Spike protein S1 | protein | 194 | 18% helix, 28% strand | P0DTC2 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.58 | 0.73 | 61 | empty |
| 2 | 219 | 0.47 | 0.75 | 29 | empty |
| 3 | 143 | 0.38 | 0.73 | 32 | empty |
| 4 | 88 | 0.35 | 0.75 | 17 | empty |
| 5 | 65 | 0.31 | 0.75 | 18 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1763 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1718 Ų buried · 16 hydrogen bonds · protein-protein
- A–R · 513 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 456 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 216 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7E7Y · Crystal structure of the SARS-CoV-2 S RBD in complex with BD-623 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 7E7Y · PDBe 7E7Y · UniProt P0DTC2
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