MolNFT v1 · #80420 · protein
Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with MAN9
3TWC · PGT127 light chain, ig lambda-2 chain C regions: “Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with MAN9”. X-ray diffraction, 2 ligands (AML, MAN), 5 pockets (best druggability 0.66). MolNFT v1…
- PDB
- 3TWC
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGT127 light chain, ig lambda-2 chain C regions; PGT127 heavy chain, ig gamma-1 chain C…
- UniProt
- P0CG05, P01857
- Ligands
- AML, MAN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | PGT127 light chain, ig lambda-2 chain C regions | protein | 208 | 7% helix, 51% strand | P0CG05 |
| H | PGT127 heavy chain, ig gamma-1 chain C region | protein | 231 | 6% helix, 52% strand | P01857 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.66 | 0.76 | 49 | empty |
| 2 | 77 | 0.42 | 0.80 | 19 | empty |
| 3 | 158 | 0.41 | 0.74 | 28 | empty |
| 4 | 78 | 0.40 | 0.78 | 21 | empty |
| 5 | 63 | 0.28 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- L–H · 1853 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 3TWC · Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with… · 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
- Every structure of UniProt P0CG05
- Every structure of UniProt P01857
- Elsewhere: RCSB PDB 3TWC · PDBe 3TWC · UniProt P0CG05 · UniProt P01857
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