Research workbench
S protein of SARS-cov-2 in complex bound with P5A-2F11_3B
Analyse S protein of SARS-cov-2 in complex bound with P5A-2F11_3B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CZZ
- Type
- protein
- Length
- 4,349 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Immunoglobulin heavy variable 1-8,IMMUNOGLOBULIN heavy variable…
- UniProt
- P0DTC2, P0DP01, V9HW68, A0A5C2G1U0, P01834
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1007 | 20% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1004 | 21% helix, 29% strand | P0DTC2 |
| H, I, J | Immunoglobulin heavy variable 1-8,IMMUNOGLOBULIN heavy variable 1-8,CHAIN H of P5A-2F11_3B,EPIDIDYMIS luminal protein 214, epididymis luminal protein 214 | protein | 224 | 3% helix, 39% strand | P0DP01, V9HW68 |
| K, M, N | Ig C168_LIGHT_IGKV4-1_IGKJ4,IMMUNOGLOBULIN kappa constant | protein | 220 | 5% helix, 30% strand | A0A5C2G1U0, P01834 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 80 copies · chains A, B, C, H, I, J
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 | 1081 | 0.85 | 0.86 | 122 | empty |
| 2 | 618 | 0.82 | 0.87 | 66 | empty |
| 3 | 440 | 0.80 | 0.88 | 64 | empty |
| 4 | 102 | 0.76 | 0.96 | 32 | empty |
| 5 | 835 | 0.75 | 0.79 | 59 | empty |
Interfaces
13 interfaces between chains.
- B–C · 4145 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 4139 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 4136 Ų buried · 39 hydrogen bonds · protein-protein
- J–N · 1814 Ų buried · 10 hydrogen bonds · protein-protein
- I–M · 1812 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7CZZ · S protein of SARS-CoV-2 in complex bound with P5A-2F11_3B · the same entry in another collection · chain N against N, TM-score 1.00
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain K against A, TM-score 0.48
- P0DP01 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy variable 1-8 (P0DP01) · a predicted model of the same protein · chain H against A, TM-score 0.42
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 P0DP01
- Every structure of UniProt V9HW68
- Every structure of UniProt A0A5C2G1U0
- Every structure of UniProt P01834
- Elsewhere: RCSB PDB 7CZZ · PDBe 7CZZ · UniProt P0DTC2 · UniProt P0DP01 · UniProt V9HW68 · UniProt A0A5C2G1U0 · UniProt P01834
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