Research workbench
Cryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human antibody 1D12 in complex with an H7 SH13 ha trimer
Analyse Cryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WXL
- Type
- protein
- Length
- 2,175 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; 1D12 light chain; 1D21 heavy chain
- UniProt
- A0A067Y6L0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Hemagglutinin HA1 chain | protein | 316 | 7% helix, 40% strand | A0A067Y6L0 |
| B, D, I | Hemagglutinin HA2 chain | protein | 170 | 50% helix, 14% strand | A0A067Y6L0 |
| L, E, J | 1D12 light chain | protein | 114 | 0% helix, 46% strand | — |
| H, F, K | 1D21 heavy chain | protein | 125 | 6% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, L, B, D, I, E, C, J, G
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 | 661 | 0.82 | 0.87 | 63 | empty |
| 2 | 183 | 0.81 | 0.95 | 27 | empty |
| 3 | 177 | 0.80 | 0.95 | 27 | empty |
| 4 | 181 | 0.80 | 0.95 | 27 | empty |
| 5 | 355 | 0.75 | 0.86 | 55 | empty |
Interfaces
36 interfaces between chains.
- I–G · 3161 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3149 Ų buried · 34 hydrogen bonds · protein-protein
- D–C · 3144 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1278 Ų buried · 8 hydrogen bonds · protein-protein
- D–I · 1274 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6WXL · Cryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human antibody 1D12 in… · the same entry in another collection · chain A against A, 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 A0A067Y6L0
- Elsewhere: RCSB PDB 6WXL · PDBe 6WXL · UniProt A0A067Y6L0
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