MolNFT v1 · #160234 · protein
Crystal structure of rabbit monoclonal anti-HIV antibody 1C2
6PEH · 1C2 Fab heavy chain: “Crystal structure of rabbit monoclonal anti-HIV antibody 1C2”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.61). MolNFT v1 #160234 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6PEH
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1C2 Fab heavy chain; 1C2 Fab light chain
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 1C2 Fab heavy chain | protein | 220 | 4% helix, 55% strand | — |
| L | 1C2 Fab light chain | protein | 213 | 6% helix, 54% strand | — |
| A | 1C2 Fab heavy chain | protein | 227 | 5% helix, 52% strand | — |
| B | 1C2 Fab light chain | protein | 214 | 5% helix, 56% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.61 | 0.75 | 55 | empty |
| 2 | 458 | 0.60 | 0.75 | 57 | empty |
| 3 | 70 | 0.44 | 0.82 | 23 | empty |
| 4 | 108 | 0.39 | 0.76 | 20 | empty |
| 5 | 96 | 0.38 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2013 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1962 Ų buried · 11 hydrogen bonds · protein-protein
- H–B · 83 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 6PEH · Crystal structure of rabbit monoclonal anti-HIV antibody 1C2 · 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 6PEH · PDBe 6PEH
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