Research workbench
Structure of SARS-cov-2 spike rbd in complex with cyclic peptide
Analyse Structure of SARS-cov-2 spike rbd in complex with cyclic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L4Z
- Type
- protein
- Length
- 1,079 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; ACE-dty-lys-ala-gly-val-val-tyr-gly-tyr-asn-ala-TRP-ile- arg-cys-NH2
- UniProt
- P0DTC2
- Ligands
- ACE, NAG, NH2
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Spike protein S1 | protein | 199 | 17% helix, 27% strand | P0DTC2 |
| D | Spike protein S1 | protein | 203 | 14% helix, 27% strand | P0DTC2 |
| C | Spike protein S1 | protein | 202 | 12% helix, 29% strand | P0DTC2 |
| E | Spike protein S1 | protein | 201 | 12% helix, 28% strand | P0DTC2 |
| S, T, R, U, V | ACE-dty-lys-ala-gly-val-val-tyr-gly-tyr-asn-ala-TRP-ile- arg-cys-NH2 | protein | 15 | 40% helix, 20% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 5 copies · chains B, S, D, T, A, R, U, V
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, S, D, T, A, R, C, E
- NH2 · Amino group · ion · 5 copies · chains B, S, T, A, R, U, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.72 | 0.96 | 22 | empty |
| 2 | 363 | 0.72 | 0.83 | 36 | empty |
| 3 | 452 | 0.65 | 0.78 | 35 | empty |
| 4 | 133 | 0.54 | 0.81 | 27 | empty |
| 5 | 144 | 0.42 | 0.75 | 36 | empty |
Interfaces
7 interfaces between chains.
- A–R · 893 Ų buried · 11 hydrogen bonds · protein-protein
- B–S · 888 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 809 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 784 Ų buried · 7 hydrogen bonds · protein-protein
- D–T · 761 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 10 covalent, 7 glycan, 5 d-amino (disulfide, covalent ligand, N-glycosylation, D-amino acid).
Compared structures
- 7L4Z · Structure of SARS-CoV-2 spike RBD in complex with cyclic peptide · the same entry in another collection · chain V against V, 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 7L4Z · PDBe 7L4Z · UniProt P0DTC2
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