MolNFT v1 · #136220 · protein
Crystal structure of HIV-1 envelope trimer 16055 nfl td cc (T569G) in complex with fabs 35022 and PGT124
5UM8 · Glycoprotein GP120: “Crystal structure of HIV-1 envelope trimer 16055 nfl td cc (T569G) in complex with fabs 35022 and PGT124”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.75). MolNFT v1 #136220 on…
- PDB
- 5UM8
- Type
- protein
- Length
- 1,498 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein GP120; Glycoprotein GP41; Fab PGT124 light chain; Fab PGT124 heavy chain…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Glycoprotein GP120 | protein | 471 | 10% helix, 37% strand | — |
| B | Glycoprotein GP41 | protein | 129 | 48% helix, 7% strand | — |
| L | Fab PGT124 light chain | protein | 211 | 7% helix, 44% strand | — |
| H | Fab PGT124 heavy chain | protein | 234 | 4% helix, 51% strand | — |
| D | Fab 35022 heavy chain | protein | 240 | 3% helix, 50% strand | — |
| E | Fab 35022 light chain | protein | 213 | 5% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 35 copies · chains G, D, L, H, B, E
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains L, H, D, E, G
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains H, D, E, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.75 | 0.79 | 80 | empty |
| 2 | 371 | 0.66 | 0.80 | 56 | NAG |
| 3 | 215 | 0.60 | 0.81 | 31 | empty |
| 4 | 456 | 0.57 | 0.73 | 59 | empty |
| 5 | 225 | 0.55 | 0.78 | 31 | empty |
Interfaces
9 interfaces between chains.
- G–B · 2660 Ų buried · 19 hydrogen bonds · protein-protein
- L–H · 2094 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1707 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 434 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 402 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 20 disulfide (N-glycosylation, disulfide).
Compared structures
- 5UM8 · Crystal structure of HIV-1 envelope trimer 16055 NFL TD CC (T569G) in complex with Fabs… · the same entry in another collection · chain G against G, 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
- Elsewhere: RCSB PDB 5UM8 · PDBe 5UM8
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