MolNFT v1 · #115284 · protein
Crystal structure of the BG505 sosip GP140 HIV-1 env trimer in complex with an early putative precursor of the PGT121 family at 3.0 ångström
5CEZ · Envelope glycoprotein GP160: “Crystal structure of the BG505 sosip GP140 HIV-1 env trimer in complex with an early putative precursor of…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 5CEZ
- Type
- protein
- Length
- 1,494 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; 3H+109L Fab light chain; 3H+109L Fab heavy chain; 35022 Fab…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 452 | 14% helix, 38% strand | Q2N0S6 |
| B | Envelope glycoprotein GP160 | protein | 147 | 54% helix, 5% strand | Q2N0S6 |
| L | 3H+109L Fab light chain | protein | 211 | 5% helix, 45% strand | — |
| H | 3H+109L Fab heavy chain | protein | 231 | 3% helix, 51% strand | — |
| D | 35022 Fab heavy chain | protein | 240 | 8% helix, 50% strand | — |
| E | 35022 Fab light chain | protein | 213 | 7% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains G, D, L, B, H, E
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains G, D, E, L, H
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.68 | 0.81 | 59 | NAG |
| 2 | 338 | 0.66 | 0.80 | 42 | empty |
| 3 | 246 | 0.63 | 0.82 | 37 | empty |
| 4 | 223 | 0.63 | 0.82 | 33 | empty |
| 5 | 172 | 0.62 | 0.84 | 28 | empty |
Interfaces
8 interfaces between chains.
- G–B · 3196 Ų buried · 30 hydrogen bonds · protein-protein
- L–H · 2040 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1672 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 5 hydrogen bonds · protein-protein
- G–D · 343 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 19 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5CEZ · Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with an early… · 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
- Every structure of UniProt Q2N0S6
- Elsewhere: RCSB PDB 5CEZ · PDBe 5CEZ · UniProt Q2N0S6
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