MolNFT v1 · #159944 · protein
HIV env BG505 nfl td+ in complex with antibody E70 fragment antigen binding
6P62 · HIV-1 env BG505 nfl td+: “HIV env BG505 nfl td+ in complex with antibody E70 fragment antigen binding”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.83). MolNFT v1 #159944 on GenesisL1: 3D…
- PDB
- 6P62
- Type
- protein
- Length
- 2,334 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 env BG505 nfl td+; Rabbit monoclonal antibody E70 heavy chain fragment antigen…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | HIV-1 env BG505 nfl td+ | protein | 551 | 24% helix, 34% strand | — |
| H, C, F | Rabbit monoclonal antibody E70 heavy chain fragment antigen binding | protein | 119 | 5% helix, 50% strand | — |
| L, D, G | Rabbit monoclonal antibody E70 kappa chain | protein | 108 | 3% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, B, E
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains H, A, L, C, B, D, F, E, G
- BMA · beta-D-mannopyranose · sugar · 6 copies
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 | 412 | 0.83 | 0.91 | 48 | empty |
| 2 | 540 | 0.76 | 0.83 | 70 | NAG |
| 3 | 307 | 0.74 | 0.86 | 49 | NAG |
| 4 | 393 | 0.73 | 0.84 | 59 | NAG |
| 5 | 80 | 0.68 | 0.93 | 24 | empty |
Interfaces
12 interfaces between chains.
- B–E · 1399 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1398 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1396 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 966 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 964 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6P62 · HIV Env BG505 NFL TD+ in complex with antibody E70 fragment antigen binding · the same entry in another collection · chain D against D, 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 6P62 · PDBe 6P62
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