Research workbench
Crystal structure of the B41 SOSIP.664 env trimer with PGT124 and 35O22 fabs, in P63 space group
Analyse Crystal structure of the B41 SOSIP.664 env trimer with PGT124 and 35O22 fabs… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MDT
- Type
- protein
- Length
- 1,486 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein GP41; Surface protein GP120; 35O22 Fab heavy chain; 35O22 Fab light…
- UniProt
- B3UES2, B3UF58
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transmembrane protein GP41 | protein | 136 | 54% helix, 5% strand | B3UES2 |
| G | Surface protein GP120 | protein | 455 | 11% helix, 36% strand | B3UF58 |
| D | 35O22 Fab heavy chain | protein | 240 | 5% helix, 49% strand | — |
| E | 35O22 Fab light chain | protein | 213 | 8% helix, 46% strand | — |
| H | PGT124 Fab heavy chain | protein | 231 | 1% helix, 50% strand | — |
| L | PGT124 Fab light chain | protein | 211 | 7% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 37 copies · chains B, D, E, G, H
- MAN · alpha-D-mannopyranose · sugar · 21 copies · chains D, E, G, H, L
- BMA · beta-D-mannopyranose · sugar · 13 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.63 | 0.80 | 31 | empty |
| 2 | 319 | 0.62 | 0.79 | 40 | empty |
| 3 | 253 | 0.62 | 0.80 | 34 | empty |
| 4 | 448 | 0.56 | 0.73 | 62 | empty |
| 5 | 217 | 0.53 | 0.77 | 26 | NAG |
Interfaces
8 interfaces between chains.
- B–G · 2809 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 2058 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1731 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 395 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 390 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 glycan, 20 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6MDT · Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63… · 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 B3UES2
- Every structure of UniProt B3UF58
- Elsewhere: RCSB PDB 6MDT · PDBe 6MDT · UniProt B3UES2 · UniProt B3UF58
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