MolNFT v1 · #89489 · protein
Crystal structure of PG16 Fab in complex with V1V2 region from HIV-1 strain ZM109
4DQO · PG16 Fab heavy chain: “Crystal structure of PG16 Fab in complex with V1V2 region from HIV-1 strain ZM109”. X-ray diffraction, 5 ligands (MAN, NAG, BMA), 7 pockets (best druggability 0.59). MolNFT v1 #89489 on GenesisL1: 3D…
- PDB
- 4DQO
- Type
- protein
- Length
- 542 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PG16 Fab heavy chain; PG16 Fab light chain; 1FD6-V1V2 scaffold ZM109 HIV-1 strain
- Ligands
- MAN, NAG, BMA, GAL, SIA
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | PG16 Fab heavy chain | protein | 240 | 9% helix, 56% strand | — |
| L | PG16 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| C | 1FD6-V1V2 scaffold ZM109 HIV-1 strain | protein | 88 | 8% helix, 48% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains H, L, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains H, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · chains H, L
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.59 | 0.73 | 64 | empty |
| 2 | 118 | 0.49 | 0.80 | 26 | empty |
| 3 | 169 | 0.47 | 0.76 | 26 | empty |
| 4 | 193 | 0.45 | 0.74 | 34 | empty |
| 5 | 69 | 0.44 | 0.82 | 20 | empty |
Interfaces
2 interfaces between chains.
- H–L · 2016 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 512 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization, sulfation).
Compared structures
- 4DQO · Crystal Structure of PG16 Fab in Complex with V1V2 Region from HIV-1 strain ZM109 · 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 4DQO · PDBe 4DQO
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