Research workbench
Crystal structure of SARS-cov-2 spike rbd in complex with MW07 Fab
Analyse Crystal structure of SARS-cov-2 spike rbd in complex with MW07 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DK2
- Type
- protein
- Length
- 2,503 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MW07 heavy chain; MW07 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MW07 heavy chain | protein | 223 | 7% helix, 49% strand | — |
| B, H, K | MW07 light chain | protein | 214 | 7% helix, 50% strand | — |
| C, L | Spike protein S1 | protein | 191 | 14% helix, 28% strand | P0DTC2 |
| D | MW07 heavy chain | protein | 222 | 7% helix, 50% strand | — |
| E | MW07 light chain | protein | 213 | 6% helix, 50% strand | — |
| F | Spike protein S1 | protein | 190 | 15% helix, 28% strand | P0DTC2 |
| G, J | MW07 heavy chain | protein | 221 | 7% helix, 50% strand | — |
| I | Spike protein S1 | protein | 189 | 15% helix, 26% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, F, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.75 | 0.95 | 28 | empty |
| 2 | 279 | 0.73 | 0.86 | 42 | empty |
| 3 | 832 | 0.71 | 0.77 | 66 | empty |
| 4 | 207 | 0.69 | 0.87 | 43 | empty |
| 5 | 88 | 0.69 | 0.93 | 26 | empty |
Interfaces
20 interfaces between chains.
- G–H · 1990 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1943 Ų buried · 11 hydrogen bonds · protein-protein
- J–K · 1942 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1816 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 737 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7DK2 · Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 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 7DK2 · PDBe 7DK2 · UniProt P0DTC2
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