Research workbench
SARS-cov-2 receptor binding domain bound to Fab wcsl 129 and Fab pdi 96
Analyse SARS-cov-2 receptor binding domain bound to Fab wcsl 129 and Fab pdi 96 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZK
- Type
- protein
- Length
- 2,130 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wcsl 129 heavy chain; Spike protein S1; Wcsl 129 light chain; Pdi 96 heavy chain; Pdi 96…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 8 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Wcsl 129 heavy chain | protein | 213 | 6% helix, 53% strand | — |
| B, A | Spike protein S1 | protein | 195 | 15% helix, 30% strand | P0DTC2 |
| E | Wcsl 129 light chain | protein | 213 | 6% helix, 47% strand | — |
| F | Wcsl 129 heavy chain | protein | 219 | 7% helix, 53% strand | — |
| N, H | Pdi 96 heavy chain | protein | 223 | 8% helix, 50% strand | — |
| M | Pdi 96 light chain | protein | 218 | 7% helix, 51% strand | — |
| L | Pdi 96 light chain | protein | 219 | 6% helix, 50% strand | — |
| D | Wcsl 129 light chain | protein | 212 | 6% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, M, A, L
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- GOL · Glycerol · additive · 3 copies · chains M, H, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B, A
- CIT · Citric acid · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.72 | 0.76 | 123 | NAG, GOL |
| 2 | 719 | 0.70 | 0.77 | 64 | MPD, GOL |
| 3 | 361 | 0.55 | 0.74 | 54 | empty |
| 4 | 259 | 0.54 | 0.76 | 44 | empty |
| 5 | 241 | 0.53 | 0.76 | 41 | empty |
Interfaces
16 interfaces between chains.
- H–L · 1879 Ų buried · 14 hydrogen bonds · protein-protein
- N–M · 1867 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1614 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1508 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 715 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7MZK · SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 96 · the same entry in another collection · chain C against C, 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 7MZK · PDBe 7MZK · UniProt P0DTC2
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