MolNFT v1 · #189609 · protein
Structure of the SARS-cov-2 spike glycoprotein in complex with a human single domain antibody N3113 (uud-state, state 2)
7VND: “Structure of the SARS-cov-2 spike glycoprotein in complex with a human single domain antibody N3113…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #189609 on GenesisL1: 3D structure, binding…
- PDB
- 7VND
- Type
- protein
- Length
- 3,442 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; N3113
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 19% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 1070 | 20% helix, 26% strand | P0DTC2 |
| V, D | N3113 | protein | 116 | 8% helix, 26% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 52 copies · chains B, A, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.87 | 0.87 | 146 | empty |
| 2 | 949 | 0.82 | 0.84 | 76 | empty |
| 3 | 619 | 0.79 | 0.85 | 64 | empty |
| 4 | 639 | 0.74 | 0.81 | 48 | empty |
| 5 | 315 | 0.74 | 0.86 | 43 | empty |
Interfaces
5 interfaces between chains.
- B–C · 4825 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 4546 Ų buried · 32 hydrogen bonds · protein-protein
- B–A · 4521 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 1050 Ų buried · 11 hydrogen bonds · protein-protein
- C–V · 830 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 glycan, 25 disulfide (N-glycosylation, disulfide).
Compared structures
- 7VND · Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain… · the same entry in another collection · chain B against B, 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 7VND · PDBe 7VND · UniProt P0DTC2
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