Research workbench
SARS-cov-2 spike protein in complex with Fab 15033-7, 2-"up"-1-"down" conformation
Analyse SARS-cov-2 spike protein in complex with Fab 15033-7, 2-"up"-1-"down"… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KXK
- Type
- protein
- Length
- 4,383 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab 15033-7 light chain; Fab 15033-7 heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1024 | 21% helix, 33% strand | P0DTC2 |
| L, M, N | Fab 15033-7 light chain | protein | 214 | 5% helix, 50% strand | — |
| H, I, J | Fab 15033-7 heavy chain | protein | 223 | 9% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 46 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.87 | 0.88 | 118 | empty |
| 2 | 1083 | 0.86 | 0.86 | 143 | empty |
| 3 | 755 | 0.77 | 0.81 | 79 | empty |
| 4 | 1176 | 0.77 | 0.79 | 106 | empty |
| 5 | 740 | 0.74 | 0.79 | 63 | empty |
Interfaces
16 interfaces between chains.
- B–C · 4561 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 4250 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3771 Ų buried · 33 hydrogen bonds · protein-protein
- L–H · 1716 Ų buried · 13 hydrogen bonds · protein-protein
- N–J · 1711 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 7KXK · SARS-CoV-2 spike protein in complex with Fab 15033-7, 2-"up"-1-"down" conformation · 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 7KXK · PDBe 7KXK · UniProt P0DTC2
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