MolNFT v1 · #36423 · protein
IGG1 Fab fragment (58.2) complex with 12-residue cyclic peptide (including residues 315-324 of HIV-1 GP120) (mn isolate)
2F58 · Protein (IGG1 Fab 58.2 antibody (light chain)): “IGG1 Fab fragment (58.2) complex with 12-residue cyclic peptide (including residues 315-324 of HIV-1 GP120)…”. X-ray diffraction, 1 ligand (ARN), 2 pockets (best druggability 0.59).…
- PDB
- 2F58
- Type
- protein
- Length
- 455 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (IGG1 Fab 58.2 antibody (light chain)); Protein (IGG1 Fab 58.2 antibody (heavy…
- Ligands
- ARN
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein (IGG1 Fab 58.2 antibody (light chain)) | protein | 216 | 6% helix, 51% strand | — |
| H | Protein (IGG1 Fab 58.2 antibody (heavy chain)) | protein | 228 | 7% helix, 53% strand | — |
| P | Protein (HIV-1 GP120) | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- ARN · 1-imino-5-pentanone · ligand · chains H, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.59 | 0.74 | 62 | empty |
| 2 | 178 | 0.49 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2005 Ų buried · 20 hydrogen bonds · protein-protein
- H–P · 425 Ų buried · 6 hydrogen bonds · protein-protein
- L–P · 344 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2F58 · IGG1 Fab fragment (58.2) complex with 12-residue cyclic peptide (including residues… · 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 2F58 · PDBe 2F58
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