MolNFT v1 · #80691 · protein
Crystal structure of PG9 Fab in complex with V1V2 region from HIV-1 strain CAP45
3U4E · V1V2 region of HIV-1 on 1FD6 scaffold: “Crystal structure of PG9 Fab in complex with V1V2 region from HIV-1 strain CAP45”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 16 pockets (best druggability 0.69). MolNFT v1 #80691 on…
- PDB
- 3U4E
- Type
- protein
- Length
- 1,112 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V1V2 region of HIV-1 on 1FD6 scaffold; PG9 heavy chain; PG9 light chain
- Ligands
- MAN, NAG, BMA, SO4
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | V1V2 region of HIV-1 on 1FD6 scaffold | protein | 108 | 16% helix, 60% strand | — |
| J | V1V2 region of HIV-1 on 1FD6 scaffold | protein | 109 | 16% helix, 61% strand | — |
| H | PG9 heavy chain | protein | 239 | 6% helix, 54% strand | — |
| L | PG9 light chain | protein | 214 | 6% helix, 49% strand | — |
| A | PG9 heavy chain | protein | 230 | 7% helix, 55% strand | — |
| B | PG9 light chain | protein | 212 | 7% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains H, L, B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains G, H, J, A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains H, A
- SO4 · Sulfate ion · ion · 12 copies · chains G, L, H, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.69 | 0.79 | 73 | MAN |
| 2 | 397 | 0.57 | 0.75 | 41 | SO4 |
| 3 | 384 | 0.56 | 0.74 | 44 | empty |
| 4 | 239 | 0.52 | 0.76 | 41 | SO4 |
| 5 | 236 | 0.51 | 0.76 | 31 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1954 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1806 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 622 Ų buried · 13 hydrogen bonds · protein-protein
- J–A · 621 Ų buried · 8 hydrogen bonds · protein-protein
- H–B · 397 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 modified, 4 glycan (disulfide, N-glycosylation, sulfation, cyclization).
Compared structures
- 3U4E · Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain CAP45 · the same entry in another collection · chain G against G, 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 3U4E · PDBe 3U4E
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