MolNFT v1 · #175732 · protein
S protein of SARS-cov-2 in complex bound with P5A-2F11_2B
7CZY · Spike glycoprotein: “S protein of SARS-cov-2 in complex bound with P5A-2F11_2B”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #175732 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7CZY
- Type
- protein
- Length
- 3,880 residues
- Chains
- 7
- 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, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1006 | 21% helix, 34% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 982 | 19% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1004 | 21% helix, 31% strand | P0DTC2 |
| H, J | Immunoglobulin heavy variable 1-8,IMMUNOGLOBULIN heavy variable 1-8,CHAIN H of P5A-2F11_2B,EPIDIDYMIS luminal protein 214, epididymis luminal protein 214 | protein | 224 | 3% helix, 39% strand | P0DP01, V9HW68 |
| K, 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 · 76 copies · chains A, B, C, H, 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 | 1050 | 0.85 | 0.86 | 128 | empty |
| 2 | 583 | 0.83 | 0.88 | 83 | empty |
| 3 | 628 | 0.82 | 0.87 | 68 | empty |
| 4 | 1191 | 0.79 | 0.81 | 92 | empty |
| 5 | 108 | 0.76 | 0.96 | 31 | empty |
Interfaces
10 interfaces between chains.
- B–C · 4577 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4212 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 4012 Ų buried · 38 hydrogen bonds · protein-protein
- H–K · 1814 Ų buried · 10 hydrogen bonds · protein-protein
- J–N · 1809 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 glycan, 44 disulfide (N-glycosylation, disulfide).
Compared structures
- 7CZY · S protein of SARS-CoV-2 in complex bound with P5A-2F11_2B · 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 7CZY · PDBe 7CZY · UniProt P0DTC2 · UniProt P0DP01 · UniProt V9HW68 · UniProt A0A5C2G1U0 · UniProt P01834
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