MolNFT v1 · #106057 · protein
Crystal structure of broadly neutralizing anti-HIV antibody PGT130
4RNR · PGT130 heavy chain: “Crystal structure of broadly neutralizing anti-HIV antibody PGT130”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.62). MolNFT v1 #106057 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4RNR
- Type
- protein
- Length
- 859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGT130 heavy chain; PGT130 light chain
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PGT130 heavy chain | protein | 218 | 7% helix, 53% strand | — |
| B, D | PGT130 light chain | protein | 212 | 8% helix, 52% strand | — |
| C | PGT130 heavy chain | protein | 217 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, C
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 | 597 | 0.62 | 0.74 | 52 | empty |
| 2 | 567 | 0.62 | 0.74 | 63 | empty |
| 3 | 316 | 0.59 | 0.78 | 37 | NAG |
| 4 | 314 | 0.56 | 0.76 | 45 | NAG |
| 5 | 123 | 0.45 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1832 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1779 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 713 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4RNR · Crystal structure of broadly neutralizing anti-HIV antibody PGT130 · 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 4RNR · PDBe 4RNR
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