Research workbench
HIV env 16055 nfl td 2CC+ in complex with antibody 1C2 fragment antigen binding
Analyse HIV env 16055 nfl td 2CC+ in complex with antibody 1C2 fragment antigen binding in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P65
- Type
- protein
- Length
- 2,379 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV env 16055 nfl td 2CC+; Rabbit antibody 1C2 heavy chain fragment antigen binding…
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | HIV env 16055 nfl td 2CC+ | protein | 557 | 25% helix, 33% strand | — |
| H, C, F | Rabbit antibody 1C2 heavy chain fragment antigen binding | protein | 126 | 6% helix, 52% strand | — |
| L, D, G | Rabbit antibody 1C2 kappa chain | protein | 110 | 0% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 111 copies · chains A, H, E, B, C, F
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains H, A, C, B, F, E
- BMA · beta-D-mannopyranose · sugar · 9 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.79 | 0.81 | 104 | empty |
| 2 | 353 | 0.79 | 0.89 | 46 | NAG |
| 3 | 373 | 0.79 | 0.88 | 46 | NAG |
| 4 | 383 | 0.79 | 0.88 | 47 | NAG |
| 5 | 632 | 0.74 | 0.80 | 82 | empty |
Interfaces
18 interfaces between chains.
- B–E · 1179 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 1172 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1171 Ų buried · 6 hydrogen bonds · protein-protein
- H–L · 1102 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1101 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6P65 · HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment antigen binding · 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
- Elsewhere: RCSB PDB 6P65 · PDBe 6P65
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