MolNFT v1 · #191368 · protein
SARS-cov-2 beta rbd in complex with human ACE2 and S304 Fab and S309 Fab
8DF5 · S309 Fab heavy chain: “SARS-cov-2 beta rbd in complex with human ACE2 and S304 Fab and S309 Fab”. X-ray diffraction, 3 ligands (NAG, ZN, CL), 20 pockets (best druggability 0.76). MolNFT v1 #191368 on GenesisL1: 3D structure, binding…
- PDB
- 8DF5
- Type
- protein
- Length
- 3,324 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S309 Fab heavy chain; S309 Fab light chain; Angiotensin-converting enzyme 2; S304 Fab…
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 10 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S309 Fab heavy chain | protein | 224 | 8% helix, 51% strand | — |
| B, D | S309 Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| C | S309 Fab heavy chain | protein | 230 | 9% helix, 49% strand | — |
| E | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 587 | 65% helix, 4% strand | Q9BYF1 |
| F | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 592 | 65% helix, 4% strand | Q9BYF1 |
| H | S304 Fab heavy chain | protein | 217 | 8% helix, 55% strand | — |
| L, N | S304 Fab light chain | protein | 215 | 7% helix, 53% strand | — |
| M | S304 Fab heavy chain | protein | 218 | 9% helix, 55% strand | — |
| R | Spike protein S1 | protein | 200 | 18% helix, 31% strand | P0DTC2 |
| S | Spike protein S1 | protein | 198 | 18% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, R, C, D, S, E, H, F
- ZN · Zinc ion · metal · 2 copies · chains E, F
- CL · Chloride ion · ion · 22 copies · chains A, B, C, D, S, E, F, H, L, N, R
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B, C, D, E, R, F, S, L, N, M
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 | 142 | 0.76 | 0.94 | 35 | empty |
| 2 | 806 | 0.70 | 0.76 | 61 | CL |
| 3 | 484 | 0.68 | 0.79 | 47 | empty |
| 4 | 861 | 0.67 | 0.74 | 83 | EDO |
| 5 | 683 | 0.66 | 0.75 | 67 | CL |
Interfaces
15 interfaces between chains.
- H–L · 1891 Ų buried · 15 hydrogen bonds · protein-protein
- M–N · 1820 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1671 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1630 Ų buried · 11 hydrogen bonds · protein-protein
- E–R · 952 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 8DF5 · SARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S309 Fab · the same entry in another collection · chain R against R, 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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 8DF5 · PDBe 8DF5 · UniProt Q9BYF1 · UniProt P0DTC2
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