MolNFT v1 · #176354 · protein
Crystal structure of SARS-cov-2 spike rbd in complex with MW05 Fab
7DK0 · MW05 heavy chain: “Crystal structure of SARS-cov-2 spike rbd in complex with MW05 Fab”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.55). MolNFT v1 #176354 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7DK0
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MW05 heavy chain; MW05 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MW05 heavy chain | protein | 222 | 7% helix, 48% strand | — |
| B | MW05 light chain | protein | 210 | 5% helix, 50% strand | — |
| C | Spike protein S1 | protein | 195 | 11% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.55 | 0.84 | 24 | empty |
| 2 | 140 | 0.42 | 0.75 | 29 | empty |
| 3 | 139 | 0.41 | 0.75 | 22 | empty |
| 4 | 69 | 0.38 | 0.78 | 20 | empty |
| 5 | 91 | 0.35 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1720 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 841 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 221 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7DK0 · Crystal structure of SARS-CoV-2 Spike RBD in complex with MW05 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 7DK0 · PDBe 7DK0 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.