Research workbench
Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 ufo-bg env trimer in complex with broadly neutralizing fabs PGT124 and 35O22 at 4.6 ångström
Analyse Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 ufo-bg env trimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CE0
- Type
- protein
- Length
- 1,473 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; 35O22 heavy chain; 35O22 light chain; PGT124 heavy chain…
- UniProt
- Q2N0T3, Q2N0S5, A4ZPX1
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP160 | protein | 137 | 55% helix, 5% strand | Q2N0T3, Q2N0S5 |
| G | Envelope glycoprotein GP160 | protein | 446 | 12% helix, 37% strand | A4ZPX1 |
| D | 35O22 heavy chain | protein | 240 | 5% helix, 48% strand | — |
| E | 35O22 light chain | protein | 213 | 6% helix, 47% strand | — |
| H | PGT124 heavy chain | protein | 226 | 3% helix, 52% strand | — |
| L | PGT124 light chain | protein | 211 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 31 copies · chains B, G, L, D, H
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains G, D, E, H, L
- BMA · beta-D-mannopyranose · sugar · 6 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 | 57 | 0.71 | 0.97 | 24 | empty |
| 2 | 168 | 0.67 | 0.87 | 32 | empty |
| 3 | 337 | 0.64 | 0.80 | 42 | empty |
| 4 | 232 | 0.64 | 0.82 | 33 | empty |
| 5 | 331 | 0.63 | 0.79 | 47 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2912 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1800 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1648 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 441 Ų buried · 8 hydrogen bonds · protein-protein
- G–D · 411 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 glycan, 20 disulfide (N-glycosylation, disulfide, glycosylation, glycation).
Compared structures
- 6CE0 · Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 UFO-BG Env trimer in complex… · 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 Q2N0T3
- Every structure of UniProt Q2N0S5
- Every structure of UniProt A4ZPX1
- Elsewhere: RCSB PDB 6CE0 · PDBe 6CE0 · UniProt Q2N0T3 · UniProt Q2N0S5 · UniProt A4ZPX1
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