Research workbench
Crystal structure of 253-11 sosip trimer in complex with 10-1074 Fab
Analyse Crystal structure of 253-11 sosip trimer in complex with 10-1074 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CCB
- Type
- protein
- Length
- 2,024 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein 41; Glycoprotein 120; 10-1074 Fab heavy chain; 10-1074 Fab light chain
- UniProt
- B2YFS0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycoprotein 41 | protein | 131 | 63% helix, 7% strand | B2YFS0 |
| C, G | Glycoprotein 120 | protein | 440 | 12% helix, 35% strand | B2YFS0 |
| D, H | 10-1074 Fab heavy chain | protein | 230 | 5% helix, 49% strand | — |
| E, L | 10-1074 Fab light chain | protein | 211 | 7% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains C, D, G, H, A, B, E, L
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains C, D, E, H, L
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, D, G, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.85 | 0.88 | 78 | empty |
| 2 | 128 | 0.77 | 0.95 | 41 | empty |
| 3 | 96 | 0.76 | 0.96 | 33 | empty |
| 4 | 1144 | 0.72 | 0.76 | 97 | empty |
| 5 | 177 | 0.69 | 0.88 | 25 | empty |
Interfaces
12 interfaces between chains.
- B–G · 2705 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 2660 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 2092 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 2035 Ų buried · 11 hydrogen bonds · protein-protein
- E–L · 798 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 glycan, 32 disulfide (N-glycosylation, disulfide).
Compared structures
- 6CCB · Crystal structure of 253-11 SOSIP trimer in complex with 10-1074 Fab · the same entry in another collection · chain A against A, 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 B2YFS0
- Elsewhere: RCSB PDB 6CCB · PDBe 6CCB · UniProt B2YFS0
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