Research workbench
HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B
Analyse HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U59
- Type
- protein
- Length
- 2,412 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SOSIP.664 GP120,SOSIP.664 GP120; SOSIP.664 GP41; Rabbit antibody 13B fragment antigen…
- UniProt
- B3UES2, B3UEZ6
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | SOSIP.664 GP120,SOSIP.664 GP120 | protein | 454 | 12% helix, 40% strand | B3UES2 |
| B, D, I | SOSIP.664 GP41 | protein | 120 | 57% helix, 3% strand | B3UEZ6 |
| L, E, J | Rabbit antibody 13B fragment antigen binding light chain | protein | 112 | 5% helix, 48% strand | — |
| H, F, K | Rabbit antibody 13B fragment antigen binding heavy chain | protein | 118 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 108 copies · chains A, H, C, F, G, K, B, D, I
- BMA · beta-D-mannopyranose · sugar · 6 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.86 | 0.88 | 120 | empty |
| 2 | 422 | 0.74 | 0.84 | 67 | NAG |
| 3 | 328 | 0.73 | 0.85 | 53 | NAG |
| 4 | 331 | 0.73 | 0.85 | 54 | NAG |
| 5 | 1040 | 0.70 | 0.74 | 82 | empty |
Interfaces
24 interfaces between chains.
- C–D · 2794 Ų buried · 23 hydrogen bonds · protein-protein
- G–I · 2788 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2785 Ų buried · 23 hydrogen bonds · protein-protein
- L–H · 1005 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 998 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 69 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 6U59 · HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B · 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 B3UES2
- Every structure of UniProt B3UEZ6
- Elsewhere: RCSB PDB 6U59 · PDBe 6U59 · UniProt B3UES2 · UniProt B3UEZ6
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