Research workbench
Crystal structure of HIV-1 CAP256 rns-3MUT-2G-SOSIP.664 prefusion env trimer in complex with human antibodies 3H109L and 35O22 at 3.5 ångström
Analyse Crystal structure of HIV-1 CAP256 rns-3MUT-2G-SOSIP.664 prefusion env trimer in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VZI
- Type
- protein
- Length
- 1,215 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP41; 35O22 scfv heavy chain; 35O22 scfv light chain; Envelope…
- UniProt
- W6ICH7, A0A0N9FF17
- Ligands
- NAG, MAN, BMA
- Pockets
- 16 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP41 | protein | 120 | 50% helix, 6% strand | W6ICH7 |
| D | 35O22 scfv heavy chain | protein | 128 | 0% helix, 45% strand | — |
| E | 35O22 scfv light chain | protein | 107 | 3% helix, 38% strand | — |
| G | Envelope glycoprotein GP160 | protein | 423 | 15% helix, 42% strand | A0A0N9FF17 |
| H | 3H109L Fab heavy chain | protein | 226 | 7% helix, 52% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 6% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains B, D, G, L, H
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains D, E, H, L
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.60 | 0.84 | 30 | empty |
| 2 | 228 | 0.60 | 0.80 | 38 | empty |
| 3 | 242 | 0.58 | 0.79 | 35 | empty |
| 4 | 265 | 0.57 | 0.77 | 24 | empty |
| 5 | 50 | 0.57 | 0.91 | 20 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2667 Ų buried · 30 hydrogen bonds · protein-protein
- H–L · 1996 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 906 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 420 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 348 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6VZI · Crystal Structure of HIV-1 CAP256 RnS-3mut-2G-SOSIP.664 Prefusion 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 W6ICH7
- Every structure of UniProt A0A0N9FF17
- Elsewhere: RCSB PDB 6VZI · PDBe 6VZI · UniProt W6ICH7 · UniProt A0A0N9FF17
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