MolNFT v1 · #156699 · protein
Crystal structure of the B41 SOSIP.664 env trimer with PGT124 and 35O22 fabs, in P23 space group
6MCO · Transmembrane protein GP41: “Crystal structure of the B41 SOSIP.664 env trimer with PGT124 and 35O22 fabs, in P23 space group”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.65). MolNFT v1 #156699 on…
- PDB
- 6MCO
- Type
- protein
- Length
- 1,484 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein GP41; 35O22 Fab heavy chain; 35O22 Fab light chain; Surface protein…
- UniProt
- B3UF08, B3UES2
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transmembrane protein GP41 | protein | 133 | 52% helix, 5% strand | B3UF08 |
| D | 35O22 Fab heavy chain | protein | 240 | 4% helix, 50% strand | — |
| E | 35O22 Fab light chain | protein | 213 | 8% helix, 45% strand | — |
| G | Surface protein GP120 | protein | 456 | 11% helix, 35% strand | B3UES2 |
| H | PGT124 Fab heavy chain | protein | 231 | 3% helix, 48% strand | — |
| L | PGT124 Fab light chain | protein | 211 | 7% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains B, D, E, G, L, H
- MAN · alpha-D-mannopyranose · sugar · 17 copies · chains E, D, H, L, G
- BMA · beta-D-mannopyranose · sugar · 12 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.65 | 0.86 | 29 | empty |
| 2 | 435 | 0.63 | 0.77 | 42 | empty |
| 3 | 285 | 0.60 | 0.79 | 45 | empty |
| 4 | 376 | 0.56 | 0.74 | 57 | empty |
| 5 | 346 | 0.53 | 0.73 | 44 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2869 Ų buried · 26 hydrogen bonds · protein-protein
- H–L · 2059 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1782 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 364 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 330 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 20 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6MCO · Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P23… · 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 B3UF08
- Every structure of UniProt B3UES2
- Elsewhere: RCSB PDB 6MCO · PDBe 6MCO · UniProt B3UF08 · UniProt B3UES2
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