MolNFT v1 · #23410 · protein
Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a 13-residue peptide containing the 4E10 epitope on GP41
1TZG: “Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a 13-residue peptide containing the…”. X-ray diffraction, 8 pockets (best druggability 0.59). MolNFT v1 #23410 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1TZG
- Type
- protein
- Length
- 912 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 4E10; Envelope polyprotein GP160
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Fab 4E10 | protein | 214 | 7% helix, 49% strand | — |
| H | Fab 4E10 | protein | 232 | 9% helix, 51% strand | — |
| I | Fab 4E10 | protein | 228 | 7% helix, 51% strand | — |
| P, Q | Envelope polyprotein GP160 | protein | 12 | 67% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.59 | 0.77 | 40 | empty |
| 2 | 457 | 0.58 | 0.74 | 53 | empty |
| 3 | 291 | 0.58 | 0.77 | 36 | empty |
| 4 | 375 | 0.57 | 0.75 | 49 | empty |
| 5 | 140 | 0.47 | 0.78 | 23 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1750 Ų buried · 14 hydrogen bonds · protein-protein
- M–I · 1685 Ų buried · 15 hydrogen bonds · protein-protein
- I–Q · 493 Ų buried · 3 hydrogen bonds · protein-protein
- H–P · 489 Ų buried · 4 hydrogen bonds · protein-protein
- M–Q · 215 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1TZG · Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a 13-residue… · the same entry in another collection · chain L against L, 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 1TZG · PDBe 1TZG
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