MolNFT v1 · #176521 · protein
Crystal structure of SARS-cov-2 spike rbd in complex with MW06 Fab
7DPM · Heavy chain of MW06: “Crystal structure of SARS-cov-2 spike rbd in complex with MW06 Fab”. X-ray diffraction, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.74). MolNFT v1 #176521 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DPM
- Type
- protein
- Length
- 2,531 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of MW06; Light chain of MW06; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain of MW06 | protein | 230 | 9% helix, 50% strand | — |
| B, E, H | Light chain of MW06 | protein | 214 | 7% helix, 50% strand | — |
| C | Spike protein S1 | protein | 196 | 16% helix, 29% strand | P0DTC2 |
| D, G | Heavy chain of MW06 | protein | 228 | 8% helix, 51% strand | — |
| F, I, L | Spike protein S1 | protein | 195 | 14% helix, 30% strand | P0DTC2 |
| J | Heavy chain of MW06 | protein | 210 | 9% helix, 50% strand | — |
| K | Light chain of MW06 | protein | 212 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C, F, I, L
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.97 | 22 | empty |
| 2 | 335 | 0.71 | 0.83 | 65 | empty |
| 3 | 54 | 0.68 | 0.96 | 18 | empty |
| 4 | 274 | 0.66 | 0.82 | 41 | empty |
| 5 | 333 | 0.59 | 0.77 | 36 | empty |
Interfaces
18 interfaces between chains.
- G–H · 2201 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2140 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1981 Ų buried · 11 hydrogen bonds · protein-protein
- J–K · 1767 Ų buried · 8 hydrogen bonds · protein-protein
- F–L · 803 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7DPM · Crystal structure of SARS-CoV-2 Spike RBD in complex with MW06 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 7DPM · PDBe 7DPM · UniProt P0DTC2
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