MolNFT v1 · #156735 · protein
Crystal structure of the B41 SOSIP.664 env trimer with PGT124 and 35O22 fabs, in P63 space group
6MDT · Transmembrane protein GP41: “Crystal structure of the B41 SOSIP.664 env trimer with PGT124 and 35O22 fabs, in P63 space group”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.63). MolNFT v1 #156735 on…
- 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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