MolNFT v1 · #157291 · protein
Crystal structure of HIV-1 B41 SOSIP.664 prefusion env trimer in complex with human antibodies 3H109L and 35O22 at 3.4 ångström
6MUF · Envelope glycoprotein GP160: “Crystal structure of HIV-1 B41 SOSIP.664 prefusion env trimer in complex with human antibodies 3H109L and…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 16 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 6MUF
- Type
- protein
- Length
- 1,220 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; 35O22 scfv heavy chain portion; 35O22 scfv light chain…
- UniProt
- B3UEZ6, B3UES2
- Ligands
- NAG, MAN, BMA
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP160 | protein | 122 | 55% helix, 7% strand | B3UEZ6 |
| D | 35O22 scfv heavy chain portion | protein | 128 | 5% helix, 40% strand | — |
| E | 35O22 scfv light chain portion | protein | 112 | 3% helix, 45% strand | — |
| G | Envelope glycoprotein GP160 | protein | 421 | 11% helix, 43% strand | B3UES2 |
| H | 3H109L Fab heavy chain | protein | 226 | 7% helix, 50% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 5% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains B, D, G, H
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains D, E, H, L
- BMA · beta-D-mannopyranose · sugar · 3 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 | 332 | 0.69 | 0.82 | 54 | NAG |
| 2 | 56 | 0.67 | 0.96 | 25 | empty |
| 3 | 255 | 0.60 | 0.79 | 31 | empty |
| 4 | 221 | 0.58 | 0.80 | 35 | empty |
| 5 | 170 | 0.55 | 0.80 | 31 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2643 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1943 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 966 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 386 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 289 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 19 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6MUF · Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human… · the same entry in another collection · chain D against D, 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 B3UEZ6
- Every structure of UniProt B3UES2
- Elsewhere: RCSB PDB 6MUF · PDBe 6MUF · UniProt B3UEZ6 · UniProt B3UES2
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