Research workbench
H11-D4, SARS-cov-2 rbd, CR3022 ternary complex
Analyse H11-D4, SARS-cov-2 rbd, CR3022 ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z2M
- Type
- protein
- Length
- 1,516 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; CR3022 antibody; Nanobody D4
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 197 | 13% helix, 28% strand | P0DTC2 |
| B, H | CR3022 antibody | protein | 216 | 8% helix, 50% strand | — |
| C, L | CR3022 antibody | protein | 219 | 3% helix, 51% strand | — |
| E | Spike glycoprotein | protein | 195 | 13% helix, 29% strand | P0DTC2 |
| F, D | Nanobody D4 | protein | 127 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, L, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.76 | 0.81 | 77 | empty |
| 2 | 445 | 0.73 | 0.83 | 54 | empty |
| 3 | 366 | 0.69 | 0.82 | 54 | empty |
| 4 | 296 | 0.69 | 0.83 | 41 | empty |
| 5 | 180 | 0.60 | 0.83 | 27 | empty |
Interfaces
13 interfaces between chains.
- B–C · 1809 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1777 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 9 hydrogen bonds · protein-protein
- E–H · 707 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 649 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z2M · H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex · the same entry in another collection · chain B against B, 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 6Z2M · PDBe 6Z2M · UniProt P0DTC2
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