MolNFT v1 · #136468 · protein
Crystal structure of a stabilized ds-SOSIP.MUT4 BG505 GP140 HIV-1 env trimer, containing mutations I201C-P433C (ds), L154M, N300M, N302M, T320L in complex with human antibodies PGT122 and 35O22 at 4.1 ångström
5UTY · HIV-1 BG505 strain env GP41: “Crystal structure of a stabilized ds-SOSIP.MUT4 BG505 GP140 HIV-1 env trimer, containing mutations…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.68). MolNFT v1 #136468…
- PDB
- 5UTY
- Type
- protein
- Length
- 1,466 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 BG505 strain env GP41; 35O22 Fab heavy chain; 35O22 Fab light chain; HIV-1 BG505…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | HIV-1 BG505 strain env GP41 | protein | 122 | 61% helix, 5% strand | Q2N0S6 |
| D | 35O22 Fab heavy chain | protein | 242 | 2% helix, 43% strand | — |
| E | 35O22 Fab light chain | protein | 213 | 2% helix, 45% strand | — |
| G | HIV-1 BG505 strain env GP120 | protein | 449 | 12% helix, 36% strand | Q2N0S6 |
| H | PGT122 Fab heavy chain | protein | 232 | 4% helix, 43% strand | — |
| L | PGT122 Fab light chain | protein | 208 | 7% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains B, D, G, H, L, E
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains D, E, H, G, L
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.68 | 0.83 | 50 | NAG |
| 2 | 126 | 0.67 | 0.89 | 24 | empty |
| 3 | 308 | 0.66 | 0.81 | 45 | NAG |
| 4 | 253 | 0.61 | 0.81 | 36 | empty |
| 5 | 258 | 0.61 | 0.80 | 25 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2672 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 2048 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1595 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 420 Ų buried · 2 hydrogen bonds · protein-protein
- G–L · 360 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 22 glycan (disulfide, N-glycosylation).
Compared structures
- 5UTY · Crystal Structure of a Stabilized DS-SOSIP.mut4 BG505 gp140 HIV-1 Env Trimer, Containing… · the same entry in another collection · chain B against B, 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 5UTY · PDBe 5UTY · UniProt Q2N0S6
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