MolNFT v1 · #92386 · protein
Crystal structure of 10E8 Fab in complex with an HIV-1 GP41 peptide
4G6F · 10E8 heavy chain: “Crystal structure of 10E8 Fab in complex with an HIV-1 GP41 peptide”. X-ray diffraction, 9 pockets (best druggability 0.77). MolNFT v1 #92386 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4G6F
- Type
- protein
- Length
- 946 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10E8 heavy chain; 10E8 light chain; GP41 mper peptide
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 10E8 heavy chain | protein | 232 | 9% helix, 51% strand | — |
| B | 10E8 heavy chain | protein | 235 | 9% helix, 51% strand | — |
| L | 10E8 light chain | protein | 212 | 8% helix, 50% strand | — |
| D | 10E8 light chain | protein | 211 | 8% helix, 50% strand | — |
| P | GP41 mper peptide | protein | 29 | 79% helix, 0% strand | — |
| F | GP41 mper peptide | protein | 27 | 78% helix, 0% strand | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.77 | 0.81 | 88 | empty |
| 2 | 462 | 0.61 | 0.75 | 62 | empty |
| 3 | 485 | 0.58 | 0.74 | 53 | empty |
| 4 | 448 | 0.55 | 0.72 | 44 | empty |
| 5 | 223 | 0.54 | 0.77 | 25 | empty |
Interfaces
9 interfaces between chains.
- H–L · 2167 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 2145 Ų buried · 21 hydrogen bonds · protein-protein
- H–P · 733 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 664 Ų buried · 7 hydrogen bonds · protein-protein
- B–L · 406 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4G6F · Crystal Structure of 10E8 Fab in Complex with an HIV-1 gp41 Peptide · the same entry in another collection · chain H against H, 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 4G6F · PDBe 4G6F
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