Research workbench
Cryo-EM structure of M1214_N1 Fab in complex with CH505 tf chimeric SOSIP.664 env trimer
Analyse Cryo-EM structure of M1214_N1 Fab in complex with CH505 tf chimeric SOSIP.664… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VY2
- Type
- protein
- Length
- 2,442 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein 120; Glycoprotein 41; M1214 N1 Fab heavy chain; M1214 N1 Fab light chain
- UniProt
- A0A0A7I3C6, Q2N0S5
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Glycoprotein 120 | protein | 458 | 14% helix, 37% strand | A0A0A7I3C6 |
| B, D, F | Glycoprotein 41 | protein | 121 | 64% helix, 6% strand | Q2N0S5 |
| H, I, J | M1214 N1 Fab heavy chain | protein | 125 | 7% helix, 62% strand | — |
| L, M, N | M1214 N1 Fab light chain | protein | 110 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 120 copies · chains A, B, C, L, H, D, E, M, I, F, N, J
- BMA · beta-D-mannopyranose · sugar · 33 copies · chains A, C, E
- MAN · alpha-D-mannopyranose · sugar · 27 copies · chains L, H, A, M, I, C, N, J, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.80 | 0.88 | 55 | empty |
| 2 | 343 | 0.74 | 0.85 | 55 | empty |
| 3 | 136 | 0.74 | 0.93 | 25 | empty |
| 4 | 123 | 0.73 | 0.92 | 33 | empty |
| 5 | 132 | 0.73 | 0.92 | 26 | empty |
Interfaces
21 interfaces between chains.
- A–B · 2200 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 2185 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 2149 Ų buried · 8 hydrogen bonds · protein-protein
- C–I · 912 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 903 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 6VY2 · Cryo-EM structure of M1214_N1 Fab in complex with CH505 TF chimeric SOSIP.664 Env trimer · 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 A0A0A7I3C6
- Every structure of UniProt Q2N0S5
- Elsewhere: RCSB PDB 6VY2 · PDBe 6VY2 · UniProt A0A0A7I3C6 · UniProt Q2N0S5
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