Research workbench
Cryo-EM structure of M4008_N1 Fab in complex with BG505 ds-SOSIP.664 env trimer
Analyse Cryo-EM structure of M4008_N1 Fab in complex with BG505 ds-SOSIP.664 env trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RAI
- Type
- protein
- Length
- 2,424 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41; M4008_N1…
- UniProt
- Q2N0S6
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 12% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Envelope glycoprotein GP160 | protein | 448 | 8% helix, 34% strand | Q2N0S6 |
| B, D, F | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 128 | 47% helix, 5% strand | Q2N0S6 |
| H, I, J | M4008_N1 Fab heavy chain | protein | 124 | 2% helix, 48% strand | — |
| L, M, N | M4008_N1 Fab light chain | protein | 108 | 0% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, E, J, H, L, C, I, M, N, B, D, F
- BMA · beta-D-mannopyranose · sugar · 21 copies · chains L, M, N
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains L, A, H, M, C, I, N, E, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.76 | 0.80 | 81 | empty |
| 2 | 1036 | 0.76 | 0.78 | 102 | empty |
| 3 | 659 | 0.75 | 0.81 | 70 | empty |
| 4 | 575 | 0.70 | 0.79 | 61 | empty |
| 5 | 83 | 0.64 | 0.91 | 22 | empty |
Interfaces
24 interfaces between chains.
- E–F · 2681 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2671 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2663 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 946 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 941 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RAI · Cryo-EM structure of M4008_N1 Fab in complex with BG505 DS-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 Q2N0S6
- Elsewhere: RCSB PDB 7RAI · PDBe 7RAI · UniProt Q2N0S6
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