MolNFT v1 · #189834 · protein
Crystal structure of SARS-cov-2 spike rbd in complex with the D27 neutralizing antibody Fab fragment
7VYR · D27 heavy chain: “Crystal structure of SARS-cov-2 spike rbd in complex with the D27 neutralizing antibody Fab fragment”. X-ray diffraction, 13 pockets (best druggability 0.76). MolNFT v1 #189834 on GenesisL1: 3D structure, binding…
- PDB
- 7VYR
- Type
- protein
- Length
- 1,238 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D27 heavy chain; D27 light chain; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | D27 heavy chain | protein | 219 | 6% helix, 49% strand | — |
| L, B | D27 light chain | protein | 214 | 7% helix, 50% strand | — |
| R, C | Spike protein S1 | protein | 186 | 14% helix, 25% strand | P0DTC2 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.76 | 0.79 | 94 | empty |
| 2 | 229 | 0.63 | 0.83 | 38 | empty |
| 3 | 284 | 0.60 | 0.79 | 37 | empty |
| 4 | 472 | 0.59 | 0.74 | 54 | empty |
| 5 | 297 | 0.58 | 0.78 | 35 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1766 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1761 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 13 hydrogen bonds · protein-protein
- H–R · 573 Ų buried · 12 hydrogen bonds · protein-protein
- L–R · 537 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 7VYR · Crystal structure of SARS-CoV-2 Spike RBD in complex with the D27 neutralizing antibody… · the same entry in another collection · chain H against H, 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 7VYR · PDBe 7VYR · UniProt P0DTC2
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