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Crystal structure at 3.4 a resolution of fully glycosylated HIV-1 clade G X1193.C1 SOSIP.664 prefusion env trimer in complex with broadly neutralizing antibodies PGT122, 35O22 and VRC01
Analyse Crystal structure at 3.4 a resolution of fully glycosylated HIV-1 clade G… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FYJ
- Type
- protein
- Length
- 1,743 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP41 env ectodomain; 35O22; GP120 env ectodomain; PGT122; VRC01
- UniProt
- C6ZIG9
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | GP41 env ectodomain | protein | 154 | 56% helix, 5% strand | C6ZIG9 |
| D | 35O22 | protein | 242 | 1% helix, 40% strand | — |
| E | 35O22 | protein | 213 | 5% helix, 43% strand | — |
| G | GP120 env ectodomain | protein | 479 | 11% helix, 36% strand | C6ZIG9 |
| H | PGT122 | protein | 228 | 4% helix, 49% strand | — |
| L | PGT122 | protein | 210 | 5% helix, 40% strand | — |
| U | VRC01 | protein | 119 | 3% helix, 45% strand | — |
| V | VRC01 | protein | 98 | 3% helix, 33% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 91 copies · chains D, E, L, G, V, H, U
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains B, E, D, G, U, V, L, H
- BMA · beta-D-mannopyranose · sugar · 20 copies · chains D, E, U, G, V, H
- CIT · Citric acid · additive · 3 copies · chains B, G, U
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.74 | 0.82 | 52 | CIT |
| 2 | 283 | 0.71 | 0.85 | 38 | CIT |
| 3 | 677 | 0.71 | 0.78 | 65 | EDO |
| 4 | 614 | 0.71 | 0.79 | 66 | empty |
| 5 | 595 | 0.62 | 0.74 | 51 | empty |
Interfaces
11 interfaces between chains.
- B–G · 2941 Ų buried · 37 hydrogen bonds · protein-protein
- H–L · 1965 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1841 Ų buried · 11 hydrogen bonds · protein-protein
- G–U · 1099 Ų buried · 20 hydrogen bonds · protein-protein
- U–V · 869 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 glycan, 25 disulfide (N-glycosylation, disulfide).
Compared structures
- 5FYJ · Crystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1 Clade G X1193.c1… · 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 C6ZIG9
- Elsewhere: RCSB PDB 5FYJ · PDBe 5FYJ · UniProt C6ZIG9
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