Research workbench
Cryo-EM structure of 2909 Fab in complex with 3BNC117 Fab and CAP256.WK34.C80 SOSIP.RNS2 N160K HIV-1 env trimer
Analyse Cryo-EM structure of 2909 Fab in complex with 3BNC117 Fab and CAP256.WK34.C80… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LY9
- Type
- protein
- Length
- 2,538 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2909 light chain; 2909 heavy chain; Envelope glycoprotein GP120; 3BNC117 heavy chain…
- UniProt
- A0A0N9FF17
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 11 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 2909 light chain | protein | 105 | 6% helix, 34% strand | — |
| H | 2909 heavy chain | protein | 129 | 2% helix, 40% strand | — |
| G | Envelope glycoprotein GP120 | protein | 436 | 12% helix, 36% strand | A0A0N9FF17 |
| B, E, A | 3BNC117 heavy chain | protein | 121 | 2% helix, 41% strand | — |
| C, I | 3BNC117 light chain | protein | 98 | 0% helix, 34% strand | — |
| F | Envelope glycoprotein GP41 | protein | 113 | 65% helix, 2% strand | A0A0N9FF17 |
| D | Envelope glycoprotein GP120 | protein | 435 | 10% helix, 35% strand | A0A0N9FF17 |
| J | Envelope glycoprotein GP41 | protein | 116 | 66% helix, 4% strand | A0A0N9FF17 |
| K | Envelope glycoprotein GP120 | protein | 435 | 11% helix, 34% strand | A0A0N9FF17 |
| M | 3BNC117 light chain | protein | 96 | 0% helix, 43% strand | — |
| N | Envelope glycoprotein GP41 | protein | 114 | 61% helix, 4% strand | A0A0N9FF17 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains G, C, D, I, K, M, B, F, L, E, J, H, A, N
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains C, G, I, M
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains C, M
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 | 1048 | 0.85 | 0.85 | 132 | empty |
| 2 | 824 | 0.77 | 0.81 | 106 | empty |
| 3 | 110 | 0.76 | 0.95 | 23 | empty |
| 4 | 471 | 0.74 | 0.83 | 49 | empty |
| 5 | 393 | 0.73 | 0.84 | 46 | empty |
Interfaces
30 interfaces between chains.
- G–F · 2664 Ų buried · 13 hydrogen bonds · protein-protein
- D–J · 2611 Ų buried · 16 hydrogen bonds · protein-protein
- K–N · 2563 Ų buried · 10 hydrogen bonds · protein-protein
- K–A · 1049 Ų buried · 7 hydrogen bonds · protein-protein
- G–B · 1014 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 40 disulfide, 2 modified (N-glycosylation, disulfide, sulfation).
Compared structures
- 7LY9 · Cryo-EM structure of 2909 Fab in complex with 3BNC117 Fab and CAP256.wk34.c80 SOSIP.RnS2… · the same entry in another collection · chain L against L, 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 A0A0N9FF17
- Elsewhere: RCSB PDB 7LY9 · PDBe 7LY9 · UniProt A0A0N9FF17
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