MolNFT v1 · #178072 · protein
SARS-cov-2 rbd in complex with A5-10 Fab and A34-2 Fab
7F3Q · Spike glycoprotein: “SARS-cov-2 rbd in complex with A5-10 Fab and A34-2 Fab”. Electron microscopy, 1 ligand (NAG), 11 pockets (best druggability 0.67). MolNFT v1 #178072 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7F3Q
- Type
- protein
- Length
- 1,050 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of A34-2 Fab; Light chain of A34-2 Fab; Heavy chain of…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.67
Structure
electron microscopy · 5 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 194 | 13% helix, 26% strand | P0DTC2 |
| H | Heavy chain of A34-2 Fab | protein | 211 | 4% helix, 49% strand | — |
| L | Light chain of A34-2 Fab | protein | 213 | 5% helix, 45% strand | — |
| C | Heavy chain of A5-10 Fab | protein | 227 | 5% helix, 45% strand | — |
| B | Light chain of A5-10 Fab | protein | 205 | 6% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.67 | 0.78 | 70 | empty |
| 2 | 53 | 0.62 | 0.93 | 17 | empty |
| 3 | 452 | 0.60 | 0.75 | 42 | empty |
| 4 | 58 | 0.58 | 0.90 | 14 | empty |
| 5 | 185 | 0.54 | 0.79 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–B · 1738 Ų buried · 10 hydrogen bonds · protein-protein
- H–L · 1701 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 573 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 393 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7F3Q · SARS-CoV-2 RBD in complex with A5-10 Fab and A34-2 Fab · the same entry in another collection · chain H against H, 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 7F3Q · PDBe 7F3Q · UniProt P0DTC2
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