MolNFT v1 · #118849 · protein
Crystal structure of PCT64_35B, a broadly neutralizing anti-HIV antibody
5FEH · PCT64_26 Fab light chain: “Crystal structure of PCT64_35B, a broadly neutralizing anti-HIV antibody”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.74). MolNFT v1 #118849 on GenesisL1: 3D structure, binding…
- PDB
- 5FEH
- Type
- protein
- Length
- 1,267 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PCT64_26 Fab light chain; PCT64_26 Fab heavy chain
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | PCT64_26 Fab light chain | protein | 212 | 6% helix, 52% strand | — |
| B | PCT64_26 Fab heavy chain | protein | 197 | 5% helix, 49% strand | — |
| C | PCT64_26 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| D | PCT64_26 Fab heavy chain | protein | 203 | 4% helix, 49% strand | — |
| F | PCT64_26 Fab heavy chain | protein | 229 | 6% helix, 55% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.74 | 0.78 | 116 | empty |
| 2 | 468 | 0.61 | 0.75 | 60 | empty |
| 3 | 421 | 0.58 | 0.75 | 53 | empty |
| 4 | 240 | 0.58 | 0.79 | 30 | empty |
| 5 | 187 | 0.56 | 0.80 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1723 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1669 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1650 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 703 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 533 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5FEH · Crystal structure of PCT64_35B, a broadly neutralizing anti-HIV antibody · 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 5FEH · PDBe 5FEH
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