Research workbench
Crystal structure of SARS-cov-2 spike rbd in complex with MW01 Fab
Analyse Crystal structure of SARS-cov-2 spike rbd in complex with MW01 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DJZ
- Type
- protein
- Length
- 635 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MW01 heavy chain; MW01 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MW01 heavy chain | protein | 225 | 4% helix, 50% strand | — |
| B | MW01 light chain | protein | 213 | 7% helix, 51% strand | — |
| C | Spike protein S1 | protein | 197 | 17% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.61 | 0.78 | 47 | empty |
| 2 | 165 | 0.53 | 0.79 | 19 | empty |
| 3 | 128 | 0.51 | 0.80 | 26 | empty |
| 4 | 236 | 0.48 | 0.74 | 33 | empty |
| 5 | 198 | 0.46 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1988 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 826 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 262 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7DJZ · Crystal structure of SARS-CoV-2 Spike RBD in complex with MW01 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 7DJZ · PDBe 7DJZ · UniProt P0DTC2
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