Research workbench
H11-H4 bound to spike
Analyse H11-H4 bound to spike in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZHD
- Type
- protein
- Length
- 3,353 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN; Nanobody H11-H4
- UniProt
- P0DTC2, P10104
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 987 | 24% helix, 33% strand | P0DTC2, P10104 |
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 992 | 23% helix, 33% strand | P0DTC2, P10104 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 990 | 24% helix, 33% strand | P0DTC2, P10104 |
| D, E, F | Nanobody H11-H4 | protein | 128 | 9% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.87 | 0.88 | 140 | empty |
| 2 | 815 | 0.85 | 0.88 | 93 | empty |
| 3 | 891 | 0.81 | 0.83 | 91 | empty |
| 4 | 902 | 0.81 | 0.83 | 85 | empty |
| 5 | 890 | 0.75 | 0.78 | 78 | empty |
Interfaces
7 interfaces between chains.
- B–C · 5057 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4801 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 4442 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 708 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 667 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZHD · H11-H4 bound to Spike · 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
- Every structure of UniProt P10104
- Elsewhere: RCSB PDB 6ZHD · PDBe 6ZHD · UniProt P0DTC2 · UniProt P10104
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